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Conserved domains on  [gi|119591922|gb|EAW71516|]
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chromodomain helicase DNA binding protein 5 [Homo sapiens]

Protein Classification

PHD finger domain-containing protein( domain architecture ID 13743289)

PHD (plant homeodomain) finger domain-containing protein; similar to the PHD domain in chromodomain-helicase-DNA-binding protein 4

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PLN03142 super family cl33647
Probable chromatin-remodeling complex ATPase chain; Provisional
698-1214 3.14e-159

Probable chromatin-remodeling complex ATPase chain; Provisional


The actual alignment was detected with superfamily member PLN03142:

Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 517.43  E-value: 3.14e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  698 GTLHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYV 777
Cdd:PLN03142  168 GKMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLGYLHEYRGITGPHMVVAPKSTLGNWMNEIRRFCPVLRA 247
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  778 VTYTGDKESRSVIRENEFsfednairsgkkvfrmkkeVQIKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQS 857
Cdd:PLN03142  248 VKFHGNPEERAHQREELL-------------------VAGKFDVCVTSFEMAIKEKTALKRFSWRYIIIDEAHRIKNENS 308
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  858 KFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISKEDQ---IKKLHDLLGPHMLRRLKA 934
Cdd:PLN03142  309 LLSKTMRLFSTNYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFQISGENDQqevVQQLHKVLRPFLLRRLKS 388
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  935 DVFKNMPAKTELIVRVELSQMQKKYYKFILTRNFEALNskGGGNQVSLLNIMMDLKKCCNHPYLFPVAAVEAPVLpngsy 1014
Cdd:PLN03142  389 DVEKGLPPKKETILKVGMSQMQKQYYKALLQKDLDVVN--AGGERKRLLNIAMQLRKCCNHPYLFQGAEPGPPYT----- 461
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922 1015 DGSSLVKSSGKLMLLQKMLKKLRDEGHRVLIFSQMTKMLDLLEDFLEYEGYKYERIDGGITGGLRQEAIDRFNAPGAQQF 1094
Cdd:PLN03142  462 TGEHLVENSGKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKF 541
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922 1095 CFLLSTRAGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQNKKVMIYRFVTRASVEERITQVAKRKMMLTHLVVR 1174
Cdd:PLN03142  542 VFLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKLALDALVIQ 621
                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*...
gi 119591922 1175 PGLGSKSGSMTKQELDDILKFGTEELFK--------DDVEGMMSQGQR 1214
Cdd:PLN03142  622 QGRLAEQKTVNKDELLQMVRYGAEMVFSskdstitdEDIDRIIAKGEE 669
CHDCT2 pfam08074
CHDCT2 (NUC038) domain; The CHDCT2 C-terminal domain is found in PHD/RING finger and chromo ...
1733-1878 5.09e-96

CHDCT2 (NUC038) domain; The CHDCT2 C-terminal domain is found in PHD/RING finger and chromo domain-associated CHD-like helicases.


:

Pssm-ID: 462358  Cd Length: 145  Bit Score: 305.90  E-value: 5.09e-96
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  1733 YDIWHRRHDYWLLAGIVTHGYARWQDIQNDPRYMILNEPFKSEVHKGNYLEMKNKFLARRFKLLEQALVIEEQLRRAAYL 1812
Cdd:pfam08074    1 YEIWHRRHDYWLLAGVATHGYGRWQDIQNDPRFSIINEPFKGESAKGNFLEIKNKFLARRFKLLEQALVIEEQLRRAAYL 80
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 119591922  1813 NMTQDPNHpAMALNARLAEVECLAESHQHLSKESLAGNKPANAVLHKVLNQLEELLSDMKADVTRL 1878
Cdd:pfam08074   81 NMQQDPSH-AGALAARFAELECLAESHQHLSKESSAGNRNANAVLHKVLNQLDELLSDMKADVSRL 145
CHDII_SANT-like pfam06461
CHD subfamily II, SANT-like domain; CHD proteins (name derived from the presence of a ...
1389-1529 4.05e-79

CHD subfamily II, SANT-like domain; CHD proteins (name derived from the presence of a Chromodomain, SWI2/SNF2 ATPase/Helicase and a motif with sequence similarity to a DNA)binding domain) are ATP-dependent chromatin remodelers found in plant and animals. In eukaryotes, there are three subfamilies, I, II and III. This domain is found in members of subfamily II which play a role in repression of genes involved in developmental regulation, including Mi-2 from Drosophila melanogaster, CHD3/4/5 from animals and PICKLE (a CHD3/4-related protein) from Arabidopsis. Sequence analysis revealed that this domain has a considerable similarity to SANT domains suggesting that it fold into this type of domain and it is integral to the DNA binding domain of CHD remodelers in subfamily II.


:

Pssm-ID: 461920  Cd Length: 137  Bit Score: 256.91  E-value: 4.05e-79
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  1389 GQSGRRQSRRQLKSDRDKPLPpLLARVGGNIEVLGFNARQRKAFLNAIMRWGMppqDAFNSHWLVRDLRGKSEKEFRAYV 1468
Cdd:pfam06461    1 PQTGRRPYRRRARVDKDEPLP-LMEGEGGSIEVLGFNARQRKAFLNALMRYGM---GNFDWKEFVRDLRGKTEKEIKAYG 76
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 119591922  1469 SLFMRHLCEPGADGAETFADGVPREGLSRQHVLTRIGVMSLVRKKVQEFEHVNGKYSTPDL 1529
Cdd:pfam06461   77 SLFLRHICEPGADNSETFADGVPKEGLSRQDVLTRIGVMSLIRKKVQEFEHIPGKPSFPDL 137
CD1_tandem_CHD3-4_like cd18667
repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and ...
465-544 2.30e-39

repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, and similar proteins; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD3 and CHD4. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. Human CHD3 (also named Mi-2 alpha) and CHD4 (also named Mi-2 beta) are coexpressed in many cell lines and tissues and may act as the motor subunit of the NuRD complex (nucleosome remodeling and deacetylase activities). The proteins form distinct CHD3- and CHD4-NuRD complexes that repress, as well as activate gene transcription of overlapping and specific target genes. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


:

Pssm-ID: 349314 [Multi-domain]  Cd Length: 79  Bit Score: 140.94  E-value: 2.30e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  465 LKGKVQRILHWRWTEPPAPfMVGLPGPDVEPSLPPPKPLEGIPEREFFVKWAGLSYWHCSWVKELQLELYHTVMYRNYQR 544
Cdd:cd18667     1 LKGKVEKILTWRWAEPPYP-EPLPEKPDEDPYPPPPRKLQPRPEREFFVKWHGMSYWHCEWVSELQLEVHHPAMYRNYQR 79
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
345-387 1.88e-30

PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the first PHD finger.


:

Pssm-ID: 277006 [Multi-domain]  Cd Length: 43  Bit Score: 114.62  E-value: 1.88e-30
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  345 YCEVCQQGGEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15531     1 YCEVCQQGGEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 43
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
418-460 7.70e-29

PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the second PHD finger.


:

Pssm-ID: 277007 [Multi-domain]  Cd Length: 43  Bit Score: 110.06  E-value: 7.70e-29
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  418 FCRVCKDGGELLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15532     1 FCRVCKDGGELLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43
CD2_tandem_CHD3-4_like cd18662
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and ...
589-642 1.23e-25

repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, and similar proteins; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD3 and CHD4, and yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. Human CHD3 (also named Mi-2 alpha) and CHD4 (also named Mi-2 beta) are coexpressed in many cell lines and tissues and may act as the motor subunit of the NuRD complex (nucleosome remodeling and deacetylase activities). The proteins form distinct CHD3- and CHD4-NuRD complexes that repress, as well as activate gene transcription of overlapping and specific target genes. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


:

Pssm-ID: 349309 [Multi-domain]  Cd Length: 55  Bit Score: 101.19  E-value: 1.23e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 119591922  589 PEWMMIHRILNHSFDKKGDVHYLIKWKDLPYDQCTWEIDDIDIPYYDNLKQAYW 642
Cdd:cd18662     1 PEWLQIHRIINHRVDKDGNTWYLVKWRDLPYDQSTWESEDDDIPDYEKHIQEYW 54
CHDNT pfam08073
CHDNT (NUC034) domain; The CHDNT domain is found in PHD/RING finger and chromo ...
145-200 1.51e-23

CHDNT (NUC034) domain; The CHDNT domain is found in PHD/RING finger and chromo domain-associated helicases.


:

Pssm-ID: 462357  Cd Length: 54  Bit Score: 95.09  E-value: 1.51e-23
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 119591922   145 DVDYlfSEEDYHTLTNYKAFSQFLRPLIAKKNPKIPMSKMMTVLGAKWREFSANNP 200
Cdd:pfam08073    1 EIDY--DEEDFQNLTTYKLFSQHVRPLLLKANPKVPMSKMMMLVAAKWREFQNHNP 54
DUF1087 pfam06465
CHD subfamily II, DUF1087; This domain is found in chromatin remodelling factors (CHDs) from ...
1298-1351 2.27e-21

CHD subfamily II, DUF1087; This domain is found in chromatin remodelling factors (CHDs) from subfamily II including CHD3/4/5 from animals and PICKLE. from Arabidopsis. The exact function is, as yet, unknown.


:

Pssm-ID: 461922  Cd Length: 60  Bit Score: 89.02  E-value: 2.27e-21
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 119591922  1298 EDGVEEVEREIIKQE-ENVDPDYWEKLLRHHYEQQQEDLARNLGKGKRIRKQVNY 1351
Cdd:pfam06465    1 AAAEEEAQKEVIKEEnESEDPNYWEKLLKHHYEQQQEEEFNALGKGKRSRKQVVS 55
 
Name Accession Description Interval E-value
PLN03142 PLN03142
Probable chromatin-remodeling complex ATPase chain; Provisional
698-1214 3.14e-159

Probable chromatin-remodeling complex ATPase chain; Provisional


Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 517.43  E-value: 3.14e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  698 GTLHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYV 777
Cdd:PLN03142  168 GKMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLGYLHEYRGITGPHMVVAPKSTLGNWMNEIRRFCPVLRA 247
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  778 VTYTGDKESRSVIRENEFsfednairsgkkvfrmkkeVQIKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQS 857
Cdd:PLN03142  248 VKFHGNPEERAHQREELL-------------------VAGKFDVCVTSFEMAIKEKTALKRFSWRYIIIDEAHRIKNENS 308
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  858 KFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISKEDQ---IKKLHDLLGPHMLRRLKA 934
Cdd:PLN03142  309 LLSKTMRLFSTNYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFQISGENDQqevVQQLHKVLRPFLLRRLKS 388
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  935 DVFKNMPAKTELIVRVELSQMQKKYYKFILTRNFEALNskGGGNQVSLLNIMMDLKKCCNHPYLFPVAAVEAPVLpngsy 1014
Cdd:PLN03142  389 DVEKGLPPKKETILKVGMSQMQKQYYKALLQKDLDVVN--AGGERKRLLNIAMQLRKCCNHPYLFQGAEPGPPYT----- 461
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922 1015 DGSSLVKSSGKLMLLQKMLKKLRDEGHRVLIFSQMTKMLDLLEDFLEYEGYKYERIDGGITGGLRQEAIDRFNAPGAQQF 1094
Cdd:PLN03142  462 TGEHLVENSGKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKF 541
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922 1095 CFLLSTRAGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQNKKVMIYRFVTRASVEERITQVAKRKMMLTHLVVR 1174
Cdd:PLN03142  542 VFLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKLALDALVIQ 621
                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*...
gi 119591922 1175 PGLGSKSGSMTKQELDDILKFGTEELFK--------DDVEGMMSQGQR 1214
Cdd:PLN03142  622 QGRLAEQKTVNKDELLQMVRYGAEMVFSskdstitdEDIDRIIAKGEE 669
DEXHc_CHD5 cd18057
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 5; ...
700-931 3.09e-157

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 5; Chromodomain-helicase-DNA-binding protein 5 (CHD5) is a chromatin-remodeling protein that binds DNA through histones and regulates gene transcription. It is thought to specifically recognize and bind trimethylated 'Lys-27' (H3K27me3) and non-methylated 'Lys-4' of histone H3 and plays a role in the development of the nervous system by activating the expression of genes promoting neuron terminal differentiation. In parallel, it may also positively regulate the trimethylation of histone H3 at 'Lys-27' thereby specifically repressing genes that promote the differentiation into non-neuronal cell lineages. As a tumor suppressor, it regulates the expression of genes involved in cell proliferation and differentiation. In spermatogenesis, it probably regulates histone hyperacetylation and the replacement of histones by transition proteins in chromatin, a crucial step in the condensation of spermatid chromatin and the production of functional spermatozoa. CHD5 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350815 [Multi-domain]  Cd Length: 232  Bit Score: 481.49  E-value: 3.09e-157
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVVT 779
Cdd:cd18057     1 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVVT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  780 YTGDKESRSVIRENEFSFEDNAIRSGKKVFRMKKEVQIKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQSKF 859
Cdd:cd18057    81 YTGDKESRSVIRENEFSFEDNAIRSGKKVFRMKKEAQIKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQSKF 160
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 119591922  860 FRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISKEDQIKKLHDLLGPHMLRR 931
Cdd:cd18057   161 FRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISKEDQIKKLHDLLGPHMLRR 232
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
697-1173 1.03e-130

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 426.18  E-value: 1.03e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  697 GGTLHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHsKGPYLVSAPLSTIINWEREFEMWAPDFY 776
Cdd:COG0553   239 KATLRPYQLEGAAWLLFLRRLGLGGLLADDMGLGKTIQALALLLELKERGL-ARPVLIVAPTSLVGNWQRELAKFAPGLR 317
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  777 VVTYTGDKESRSVIREnefsFEDnairsgkkvfrmkkevqikFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQ 856
Cdd:COG0553   318 VLVLDGTRERAKGANP----FED-------------------ADLVITSYGLLRRDIELLAAVDWDLVILDEAQHIKNPA 374
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  857 SKFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFAD-ISKEDQ--IKKLHDLLGPHMLRRLK 933
Cdd:COG0553   375 TKRAKAVRALKARHRLALTGTPVENRLEELWSLLDFLNPGLLGSLKAFRERFARpIEKGDEeaLERLRRLLRPFLLRRTK 454
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  934 ADVFKNMPAKTELIVRVELSQMQKKYYKFILTRNFEALN-SKGGGNQVSLLNIMMDLKKCCNHPYLFPVaaveapvlpng 1012
Cdd:COG0553   455 EDVLKDLPEKTEETLYVELTPEQRALYEAVLEYLRRELEgAEGIRRRGLILAALTRLRQICSHPALLLE----------- 523
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922 1013 syDGSSLVKSSGKLMLLQKMLKKLRDEGHRVLIFSQMTKMLDLLEDFLEYEGYKYERIDGGITGGLRQEAIDRFNA-PGA 1091
Cdd:COG0553   524 --EGAELSGRSAKLEALLELLEELLAEGEKVLVFSQFTDTLDLLEERLEERGIEYAYLHGGTSAEERDELVDRFQEgPEA 601
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922 1092 QQfcFLLSTRAGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQNKKVMIYRFVTRASVEERITQVAKRKMMLTHL 1171
Cdd:COG0553   602 PV--FLISLKAGGEGLNLTAADHVIHYDLWWNPAVEEQAIDRAHRIGQTRDVQVYKLVAEGTIEEKILELLEEKRALAES 679

                  ..
gi 119591922 1172 VV 1173
Cdd:COG0553   680 VL 681
CHDCT2 pfam08074
CHDCT2 (NUC038) domain; The CHDCT2 C-terminal domain is found in PHD/RING finger and chromo ...
1733-1878 5.09e-96

CHDCT2 (NUC038) domain; The CHDCT2 C-terminal domain is found in PHD/RING finger and chromo domain-associated CHD-like helicases.


Pssm-ID: 462358  Cd Length: 145  Bit Score: 305.90  E-value: 5.09e-96
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  1733 YDIWHRRHDYWLLAGIVTHGYARWQDIQNDPRYMILNEPFKSEVHKGNYLEMKNKFLARRFKLLEQALVIEEQLRRAAYL 1812
Cdd:pfam08074    1 YEIWHRRHDYWLLAGVATHGYGRWQDIQNDPRFSIINEPFKGESAKGNFLEIKNKFLARRFKLLEQALVIEEQLRRAAYL 80
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 119591922  1813 NMTQDPNHpAMALNARLAEVECLAESHQHLSKESLAGNKPANAVLHKVLNQLEELLSDMKADVTRL 1878
Cdd:pfam08074   81 NMQQDPSH-AGALAARFAELECLAESHQHLSKESSAGNRNANAVLHKVLNQLDELLSDMKADVSRL 145
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
703-999 8.10e-85

SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.


Pssm-ID: 425504 [Multi-domain]  Cd Length: 289  Bit Score: 279.95  E-value: 8.10e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922   703 YQLEGLNWLRFSWAQ-GTDTILADEMGLGKTVQTIVFLYSLYKEGHSKG-PYLVSAPLSTIINWEREFEMWA--PDFYVV 778
Cdd:pfam00176    1 YQIEGVNWMLSLENNlGRGGILADEMGLGKTLQTISLLLYLKHVDKNWGgPTLIVVPLSLLHNWMNEFERWVspPALRVV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922   779 TYTGDKESRSVIREnefsfednairsgkkvfrmKKEVQIKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQSK 858
Cdd:pfam00176   81 VLHGNKRPQERWKN-------------------DPNFLADFDVVITTYETLRKHKELLKKVHWHRIVLDEGHRLKNSKSK 141
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922   859 FFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEF-ADISKEDQ---IKKLHDLLGPHMLRRLKA 934
Cdd:pfam00176  142 LSKALKSLKTRNRWILTGTPLQNNLEELWALLNFLRPGPFGSLSTFRNWFdRPIERGGGkkgVSRLHKLLKPFLLRRTKK 221
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 119591922   935 DVFKNMPAKTELIVRVELSQMQKKYYK-FILTRNFEALNSKGGGNQV--SLLNIMMDLKKCCNHPYLF 999
Cdd:pfam00176  222 DVEKSLPPKVEYILFCRLSKLQRKLYQtFLLKKDLNAIKTGEGGREIkaSLLNILMRLRKICNHPGLI 289
CHDII_SANT-like pfam06461
CHD subfamily II, SANT-like domain; CHD proteins (name derived from the presence of a ...
1389-1529 4.05e-79

CHD subfamily II, SANT-like domain; CHD proteins (name derived from the presence of a Chromodomain, SWI2/SNF2 ATPase/Helicase and a motif with sequence similarity to a DNA)binding domain) are ATP-dependent chromatin remodelers found in plant and animals. In eukaryotes, there are three subfamilies, I, II and III. This domain is found in members of subfamily II which play a role in repression of genes involved in developmental regulation, including Mi-2 from Drosophila melanogaster, CHD3/4/5 from animals and PICKLE (a CHD3/4-related protein) from Arabidopsis. Sequence analysis revealed that this domain has a considerable similarity to SANT domains suggesting that it fold into this type of domain and it is integral to the DNA binding domain of CHD remodelers in subfamily II.


Pssm-ID: 461920  Cd Length: 137  Bit Score: 256.91  E-value: 4.05e-79
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  1389 GQSGRRQSRRQLKSDRDKPLPpLLARVGGNIEVLGFNARQRKAFLNAIMRWGMppqDAFNSHWLVRDLRGKSEKEFRAYV 1468
Cdd:pfam06461    1 PQTGRRPYRRRARVDKDEPLP-LMEGEGGSIEVLGFNARQRKAFLNALMRYGM---GNFDWKEFVRDLRGKTEKEIKAYG 76
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 119591922  1469 SLFMRHLCEPGADGAETFADGVPREGLSRQHVLTRIGVMSLVRKKVQEFEHVNGKYSTPDL 1529
Cdd:pfam06461   77 SLFLRHICEPGADNSETFADGVPKEGLSRQDVLTRIGVMSLIRKKVQEFEHIPGKPSFPDL 137
CD1_tandem_CHD3-4_like cd18667
repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and ...
465-544 2.30e-39

repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, and similar proteins; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD3 and CHD4. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. Human CHD3 (also named Mi-2 alpha) and CHD4 (also named Mi-2 beta) are coexpressed in many cell lines and tissues and may act as the motor subunit of the NuRD complex (nucleosome remodeling and deacetylase activities). The proteins form distinct CHD3- and CHD4-NuRD complexes that repress, as well as activate gene transcription of overlapping and specific target genes. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349314 [Multi-domain]  Cd Length: 79  Bit Score: 140.94  E-value: 2.30e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  465 LKGKVQRILHWRWTEPPAPfMVGLPGPDVEPSLPPPKPLEGIPEREFFVKWAGLSYWHCSWVKELQLELYHTVMYRNYQR 544
Cdd:cd18667     1 LKGKVEKILTWRWAEPPYP-EPLPEKPDEDPYPPPPRKLQPRPEREFFVKWHGMSYWHCEWVSELQLEVHHPAMYRNYQR 79
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
345-387 1.88e-30

PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the first PHD finger.


Pssm-ID: 277006 [Multi-domain]  Cd Length: 43  Bit Score: 114.62  E-value: 1.88e-30
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  345 YCEVCQQGGEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15531     1 YCEVCQQGGEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 43
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
418-460 7.70e-29

PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the second PHD finger.


Pssm-ID: 277007 [Multi-domain]  Cd Length: 43  Bit Score: 110.06  E-value: 7.70e-29
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  418 FCRVCKDGGELLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15532     1 FCRVCKDGGELLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43
CD2_tandem_CHD3-4_like cd18662
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and ...
589-642 1.23e-25

repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, and similar proteins; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD3 and CHD4, and yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. Human CHD3 (also named Mi-2 alpha) and CHD4 (also named Mi-2 beta) are coexpressed in many cell lines and tissues and may act as the motor subunit of the NuRD complex (nucleosome remodeling and deacetylase activities). The proteins form distinct CHD3- and CHD4-NuRD complexes that repress, as well as activate gene transcription of overlapping and specific target genes. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349309 [Multi-domain]  Cd Length: 55  Bit Score: 101.19  E-value: 1.23e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 119591922  589 PEWMMIHRILNHSFDKKGDVHYLIKWKDLPYDQCTWEIDDIDIPYYDNLKQAYW 642
Cdd:cd18662     1 PEWLQIHRIINHRVDKDGNTWYLVKWRDLPYDQSTWESEDDDIPDYEKHIQEYW 54
DEXDc smart00487
DEAD-like helicases superfamily;
694-902 1.37e-24

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 103.34  E-value: 1.37e-24
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922    694 DSTGGTLHPYQLEGLNWLRFSWaqgTDTILADEMGLGKTVQTIVFLYSLYKEGhSKGPYLVSAPL-STIINWEREFEMWA 772
Cdd:smart00487    3 KFGFEPLRPYQKEAIEALLSGL---RDVILAAPTGSGKTLAALLPALEALKRG-KGGRVLVLVPTrELAEQWAEELKKLG 78
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922    773 PDFY--VVTYTGDKESRSVIREnefsfednaIRSGkkvfrmkkevqiKFHVLLTSYELIT--IDQAILGSIEWACLVVDE 848
Cdd:smart00487   79 PSLGlkVVGLYGGDSKREQLRK---------LESG------------KTDILVTTPGRLLdlLENDKLSLSNVDLVILDE 137
                           170       180       190       200       210       220
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 119591922    849 AHRLKNNqsKFFRVLNSY-----KIDYKLLLTGTP---LQNNLEELFHLLNFLTPERFNNLE 902
Cdd:smart00487  138 AHRLLDG--GFGDQLEKLlkllpKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPLEP 197
CHDNT pfam08073
CHDNT (NUC034) domain; The CHDNT domain is found in PHD/RING finger and chromo ...
145-200 1.51e-23

CHDNT (NUC034) domain; The CHDNT domain is found in PHD/RING finger and chromo domain-associated helicases.


Pssm-ID: 462357  Cd Length: 54  Bit Score: 95.09  E-value: 1.51e-23
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 119591922   145 DVDYlfSEEDYHTLTNYKAFSQFLRPLIAKKNPKIPMSKMMTVLGAKWREFSANNP 200
Cdd:pfam08073    1 EIDY--DEEDFQNLTTYKLFSQHVRPLLLKANPKVPMSKMMMLVAAKWREFQNHNP 54
DUF1087 pfam06465
CHD subfamily II, DUF1087; This domain is found in chromatin remodelling factors (CHDs) from ...
1298-1351 2.27e-21

CHD subfamily II, DUF1087; This domain is found in chromatin remodelling factors (CHDs) from subfamily II including CHD3/4/5 from animals and PICKLE. from Arabidopsis. The exact function is, as yet, unknown.


Pssm-ID: 461922  Cd Length: 60  Bit Score: 89.02  E-value: 2.27e-21
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 119591922  1298 EDGVEEVEREIIKQE-ENVDPDYWEKLLRHHYEQQQEDLARNLGKGKRIRKQVNY 1351
Cdd:pfam06465    1 AAAEEEAQKEVIKEEnESEDPNYWEKLLKHHYEQQQEEEFNALGKGKRSRKQVVS 55
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
418-462 2.94e-17

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 77.15  E-value: 2.94e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 119591922   418 FCRVCK---DGGELLCCDACPSSYHLHCLNPPLP--EIPNGEWLCPRCTC 462
Cdd:pfam00628    1 YCAVCGksdDGGELVQCDGCDDWFHLACLGPPLDpaEIPSGEWLCPECKP 50
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
345-387 5.22e-15

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 70.60  E-value: 5.22e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 119591922   345 YCEVCQQ---GGEIILCDTCPRAYHLVCLDPELEKA--PEGKWSCPHC 387
Cdd:pfam00628    1 YCAVCGKsddGGELVQCDGCDDWFHLACLGPPLDPAeiPSGEWLCPEC 48
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
418-460 2.55e-14

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 68.78  E-value: 2.55e-14
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 119591922    418 FCRVCK---DGGELLCCDACPSSYHLHCLNPPL-PEIPNGEWLCPRC 460
Cdd:smart00249    1 YCSVCGkpdDGGELLQCDGCDRWYHQTCLGPPLlEEEPDGKWYCPKC 47
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
345-387 2.43e-13

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 66.08  E-value: 2.43e-13
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 119591922    345 YCEVCQQ---GGEIILCDTCPRAYHLVCLDPELEKA-PEGKWSCPHC 387
Cdd:smart00249    1 YCSVCGKpddGGELLQCDGCDRWYHQTCLGPPLLEEePDGKWYCPKC 47
Chromo pfam00385
Chromo (CHRromatin organization MOdifier) domain;
592-630 7.70e-11

Chromo (CHRromatin organization MOdifier) domain;


Pssm-ID: 459793 [Multi-domain]  Cd Length: 52  Bit Score: 58.74  E-value: 7.70e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 119591922   592 MMIHRILNHSFDKKGDVHYLIKWKDLPYDQCTWE-IDDID 630
Cdd:pfam00385    1 YEVERILDHRKDKGGKEEYLVKWKGYPYDENTWEpEENLS 40
CHROMO smart00298
Chromatin organization modifier domain;
592-625 2.38e-10

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 57.61  E-value: 2.38e-10
                            10        20        30
                    ....*....|....*....|....*....|....
gi 119591922    592 MMIHRILNHSFDKKGDVHYLIKWKDLPYDQCTWE 625
Cdd:smart00298    2 YEVEKILDHRWKKKGELEYLVKWKGYSYSEDTWE 35
CHROMO smart00298
Chromatin organization modifier domain;
466-546 3.33e-07

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 48.75  E-value: 3.33e-07
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922    466 KGKVQRILHWRWTEppapfmvglpgpdvepslpppkplEGipEREFFVKWAGLSYWHCSWVKELQLELYHTVMYRNYQRK 545
Cdd:smart00298    1 EYEVEKILDHRWKK------------------------KG--ELEYLVKWKGYSYSEDTWEPEENLLNCSKKLDNYKKKE 54

                    .
gi 119591922    546 N 546
Cdd:smart00298   55 R 55
TNG2 COG5034
Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];
334-390 1.72e-06

Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];


Pssm-ID: 227367 [Multi-domain]  Cd Length: 271  Bit Score: 51.86  E-value: 1.72e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 119591922  334 DGDGYETDHQDYCeVCQQG--GEIILCDT--CPRA-YHLVCLDpeLEKAPEGKWSCPHCEKE 390
Cdd:COG5034   212 SSEDNSEGEELYC-FCQQVsyGQMVACDNanCKREwFHLECVG--LKEPPKGKWYCPECKKA 270
 
Name Accession Description Interval E-value
PLN03142 PLN03142
Probable chromatin-remodeling complex ATPase chain; Provisional
698-1214 3.14e-159

Probable chromatin-remodeling complex ATPase chain; Provisional


Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 517.43  E-value: 3.14e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  698 GTLHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYV 777
Cdd:PLN03142  168 GKMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLGYLHEYRGITGPHMVVAPKSTLGNWMNEIRRFCPVLRA 247
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  778 VTYTGDKESRSVIRENEFsfednairsgkkvfrmkkeVQIKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQS 857
Cdd:PLN03142  248 VKFHGNPEERAHQREELL-------------------VAGKFDVCVTSFEMAIKEKTALKRFSWRYIIIDEAHRIKNENS 308
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  858 KFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISKEDQ---IKKLHDLLGPHMLRRLKA 934
Cdd:PLN03142  309 LLSKTMRLFSTNYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFQISGENDQqevVQQLHKVLRPFLLRRLKS 388
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  935 DVFKNMPAKTELIVRVELSQMQKKYYKFILTRNFEALNskGGGNQVSLLNIMMDLKKCCNHPYLFPVAAVEAPVLpngsy 1014
Cdd:PLN03142  389 DVEKGLPPKKETILKVGMSQMQKQYYKALLQKDLDVVN--AGGERKRLLNIAMQLRKCCNHPYLFQGAEPGPPYT----- 461
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922 1015 DGSSLVKSSGKLMLLQKMLKKLRDEGHRVLIFSQMTKMLDLLEDFLEYEGYKYERIDGGITGGLRQEAIDRFNAPGAQQF 1094
Cdd:PLN03142  462 TGEHLVENSGKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKF 541
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922 1095 CFLLSTRAGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQNKKVMIYRFVTRASVEERITQVAKRKMMLTHLVVR 1174
Cdd:PLN03142  542 VFLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKLALDALVIQ 621
                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*...
gi 119591922 1175 PGLGSKSGSMTKQELDDILKFGTEELFK--------DDVEGMMSQGQR 1214
Cdd:PLN03142  622 QGRLAEQKTVNKDELLQMVRYGAEMVFSskdstitdEDIDRIIAKGEE 669
DEXHc_CHD5 cd18057
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 5; ...
700-931 3.09e-157

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 5; Chromodomain-helicase-DNA-binding protein 5 (CHD5) is a chromatin-remodeling protein that binds DNA through histones and regulates gene transcription. It is thought to specifically recognize and bind trimethylated 'Lys-27' (H3K27me3) and non-methylated 'Lys-4' of histone H3 and plays a role in the development of the nervous system by activating the expression of genes promoting neuron terminal differentiation. In parallel, it may also positively regulate the trimethylation of histone H3 at 'Lys-27' thereby specifically repressing genes that promote the differentiation into non-neuronal cell lineages. As a tumor suppressor, it regulates the expression of genes involved in cell proliferation and differentiation. In spermatogenesis, it probably regulates histone hyperacetylation and the replacement of histones by transition proteins in chromatin, a crucial step in the condensation of spermatid chromatin and the production of functional spermatozoa. CHD5 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350815 [Multi-domain]  Cd Length: 232  Bit Score: 481.49  E-value: 3.09e-157
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVVT 779
Cdd:cd18057     1 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVVT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  780 YTGDKESRSVIRENEFSFEDNAIRSGKKVFRMKKEVQIKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQSKF 859
Cdd:cd18057    81 YTGDKESRSVIRENEFSFEDNAIRSGKKVFRMKKEAQIKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQSKF 160
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 119591922  860 FRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISKEDQIKKLHDLLGPHMLRR 931
Cdd:cd18057   161 FRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISKEDQIKKLHDLLGPHMLRR 232
DEXHc_CHD3 cd18055
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 3; ...
700-931 2.26e-151

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 3; Chromodomain-helicase-DNA-binding protein 3 (CHD3) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. It is required for anchoring centrosomal pericentrin in both interphase and mitosis, for spindle organization and centrosome integrity. CHD3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350813 [Multi-domain]  Cd Length: 232  Bit Score: 465.64  E-value: 2.26e-151
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVVT 779
Cdd:cd18055     1 LHMYQLEGLNWLRFSWAQGTDTILADEMGLGKTIQTIVFLYSLYKEGHTKGPFLVSAPLSTIINWEREFQMWAPDFYVVT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  780 YTGDKESRSVIRENEFSFEDNAIRSGKKVFRMKKEVQIKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQSKF 859
Cdd:cd18055    81 YTGDKDSRAIIRENEFSFDDNAVKGGKKAFKMKREAQVKFHVLLTSYELVTIDQAALGSIRWACLVVDEAHRLKNNQSKF 160
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 119591922  860 FRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISKEDQIKKLHDLLGPHMLRR 931
Cdd:cd18055   161 FRVLNGYKIDHKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISKEDQIKKLHDLLGPHMLRR 232
DEXHc_CHD4 cd18056
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 4; ...
700-931 1.61e-143

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 4; Chromodomain-helicase-DNA-binding protein 4 (CHD4) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. CHD4 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350814 [Multi-domain]  Cd Length: 232  Bit Score: 443.74  E-value: 1.61e-143
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVVT 779
Cdd:cd18056     1 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTAVFLYSLYKEGHSKGPFLVSAPLSTIINWEREFEMWAPDMYVVT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  780 YTGDKESRSVIRENEFSFEDNAIRSGKKVFRMKKEVQIKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQSKF 859
Cdd:cd18056    81 YVGDKDSRAIIRENEFSFEDNAIRGGKKASRMKKEASVKFHVLLTSYELITIDMAILGSIDWACLIVDEAHRLKNNQSKF 160
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 119591922  860 FRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISKEDQIKKLHDLLGPHMLRR 931
Cdd:cd18056   161 FRVLNGYSLQHKLLLTGTPLQNNLEELFHLLNFLTPERFHNLEGFLEEFADIAKEDQIKKLHDMLGPHMLRR 232
DEXHc_CHD3_4_5 cd17994
DEAH-box helicase domain of the chromodomain helicase DNA binding proteins 3, 4 and 5; ...
700-931 1.50e-136

DEAH-box helicase domain of the chromodomain helicase DNA binding proteins 3, 4 and 5; Chromodomain-helicase-DNA-binding protein 3 (CHD3) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. It is required for anchoring centrosomal pericentrin in both interphase and mitosis, for spindle organization and centrosome integrity. Chromodomain-helicase-DNA-binding protein 4 (CHD4) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. Chromodomain-helicase-DNA-binding protein 5 (CHD5) is a chromatin-remodeling protein that binds DNA through histones and regulates gene transcription. It is thought to specifically recognize and bind trimethylated 'Lys-27' (H3K27me3) and non-methylated 'Lys-4' of histone H3 and plays a role in the development of the nervous system by activating the expression of genes promoting neuron terminal differentiation. In parallel, it may also positively regulate the trimethylation of histone H3 at 'Lys-27' thereby specifically repressing genes that promote the differentiation into non-neuronal cell lineages. As a tumor suppressor, it regulates the expression of genes involved in cell proliferation and differentiation. In spermatogenesis, it probably regulates histone hyperacetylation and the replacement of histones by transition proteins in chromatin, a crucial step in the condensation of spermatid chromatin and the production of functional spermatozoa. CHD3, CHD4, and CHD5 are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350752 [Multi-domain]  Cd Length: 196  Bit Score: 423.00  E-value: 1.50e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVVT 779
Cdd:cd17994     1 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTIQTIVFLYSLYKEGHSKGPFLVSAPLSTIINWEREFEMWAPDFYVVT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  780 YTGDkesrsvirenefsfednairsgkkvfrmkkevqikfHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQSKF 859
Cdd:cd17994    81 YVGD------------------------------------HVLLTSYELISIDQAILGSIDWAVLVVDEAHRLKNNQSKF 124
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 119591922  860 FRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISKEDQIKKLHDLLGPHMLRR 931
Cdd:cd17994   125 FRILNSYKIGYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLQGFLEEFADISKEDQIKKLHDLLGPHMLRR 196
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
697-1173 1.03e-130

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 426.18  E-value: 1.03e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  697 GGTLHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHsKGPYLVSAPLSTIINWEREFEMWAPDFY 776
Cdd:COG0553   239 KATLRPYQLEGAAWLLFLRRLGLGGLLADDMGLGKTIQALALLLELKERGL-ARPVLIVAPTSLVGNWQRELAKFAPGLR 317
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  777 VVTYTGDKESRSVIREnefsFEDnairsgkkvfrmkkevqikFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQ 856
Cdd:COG0553   318 VLVLDGTRERAKGANP----FED-------------------ADLVITSYGLLRRDIELLAAVDWDLVILDEAQHIKNPA 374
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  857 SKFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFAD-ISKEDQ--IKKLHDLLGPHMLRRLK 933
Cdd:COG0553   375 TKRAKAVRALKARHRLALTGTPVENRLEELWSLLDFLNPGLLGSLKAFRERFARpIEKGDEeaLERLRRLLRPFLLRRTK 454
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  934 ADVFKNMPAKTELIVRVELSQMQKKYYKFILTRNFEALN-SKGGGNQVSLLNIMMDLKKCCNHPYLFPVaaveapvlpng 1012
Cdd:COG0553   455 EDVLKDLPEKTEETLYVELTPEQRALYEAVLEYLRRELEgAEGIRRRGLILAALTRLRQICSHPALLLE----------- 523
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922 1013 syDGSSLVKSSGKLMLLQKMLKKLRDEGHRVLIFSQMTKMLDLLEDFLEYEGYKYERIDGGITGGLRQEAIDRFNA-PGA 1091
Cdd:COG0553   524 --EGAELSGRSAKLEALLELLEELLAEGEKVLVFSQFTDTLDLLEERLEERGIEYAYLHGGTSAEERDELVDRFQEgPEA 601
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922 1092 QQfcFLLSTRAGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQNKKVMIYRFVTRASVEERITQVAKRKMMLTHL 1171
Cdd:COG0553   602 PV--FLISLKAGGEGLNLTAADHVIHYDLWWNPAVEEQAIDRAHRIGQTRDVQVYKLVAEGTIEEKILELLEEKRALAES 679

                  ..
gi 119591922 1172 VV 1173
Cdd:COG0553   680 VL 681
DEXHc_CHD6_7_8_9 cd17995
DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; ...
700-931 1.87e-98

DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; Chromodomain-helicase-DNA-binding protein 6-9 (CHD6, CHD7, CHD8, and CHD9) are members of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350753 [Multi-domain]  Cd Length: 223  Bit Score: 316.11  E-value: 1.87e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWApDFYVVT 779
Cdd:cd17995     1 LRDYQLEGVNWLLFNWYNRRNCILADEMGLGKTIQSIAFLEHLYQVEGIRGPFLVIAPLSTIPNWQREFETWT-DMNVVV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  780 YTGDKESRSVIRENEFSFEDNAIRSGKKVFrmkkevqiKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQSKF 859
Cdd:cd17995    80 YHGSGESRQIIQQYEMYFKDAQGRKKKGVY--------KFDVLITTYEMVIADAEELRKIPWRVVVVDEAHRLKNRNSKL 151
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 119591922  860 FRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISKEDQIKKLHDLLGPHMLRR 931
Cdd:cd17995   152 LQGLKKLTLEHKLLLTGTPLQNNTEELWSLLNFLEPEKFPSSEEFLEEFGDLKTAEQVEKLQALLKPYMLRR 223
CHDCT2 pfam08074
CHDCT2 (NUC038) domain; The CHDCT2 C-terminal domain is found in PHD/RING finger and chromo ...
1733-1878 5.09e-96

CHDCT2 (NUC038) domain; The CHDCT2 C-terminal domain is found in PHD/RING finger and chromo domain-associated CHD-like helicases.


Pssm-ID: 462358  Cd Length: 145  Bit Score: 305.90  E-value: 5.09e-96
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  1733 YDIWHRRHDYWLLAGIVTHGYARWQDIQNDPRYMILNEPFKSEVHKGNYLEMKNKFLARRFKLLEQALVIEEQLRRAAYL 1812
Cdd:pfam08074    1 YEIWHRRHDYWLLAGVATHGYGRWQDIQNDPRFSIINEPFKGESAKGNFLEIKNKFLARRFKLLEQALVIEEQLRRAAYL 80
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 119591922  1813 NMTQDPNHpAMALNARLAEVECLAESHQHLSKESLAGNKPANAVLHKVLNQLEELLSDMKADVTRL 1878
Cdd:pfam08074   81 NMQQDPSH-AGALAARFAELECLAESHQHLSKESSAGNRNANAVLHKVLNQLDELLSDMKADVSRL 145
DEXHc_CHD1_2 cd17993
DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and ...
699-931 5.61e-95

DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and similar proteins; Chromodomain-helicase-DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin-remodeling factor which functions as the substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. It regulates polymerase II transcription and is also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. It is not only involved in transcription-related chromatin-remodeling, but is also required to maintain a specific chromatin configuration across the genome. CHD1 is also associated with histone deacetylase (HDAC) activity. Chromodomain-helicase-DNA-binding protein 2 (CHD2) is a DNA-binding helicase that specifically binds to the promoter of target genes, leading to chromatin remodeling, possibly by promoting deposition of histone H3.3. It is involved in myogenesis via interaction with MYOD1; it binds to myogenic gene regulatory sequences and mediates incorporation of histone H3.3 prior to the onset of myogenic gene expression, promoting their expression. Both are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350751 [Multi-domain]  Cd Length: 218  Bit Score: 305.82  E-value: 5.61e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  699 TLHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVV 778
Cdd:cd17993     1 ELRDYQLTGLNWLAHSWCKGNNGILADEMGLGKTVQTISFLSYLFHSQQQYGPFLVVVPLSTMPAWQREFAKWAPDMNVI 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  779 TYTGDKESRSVIRENEFSFEdnairSGKKvfrmkkevqIKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQSK 858
Cdd:cd17993    81 VYLGDIKSRDTIREYEFYFS-----QTKK---------LKFNVLLTTYEIILKDKAFLGSIKWQYLAVDEAHRLKNDESL 146
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 119591922  859 FFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFlEEFADISKEDQIKKLHDLLGPHMLRR 931
Cdd:cd17993   147 LYEALKEFKTNNRLLITGTPLQNSLKELWALLHFLMPGKFDIWEEF-EEEHDEEQEKGIADLHKELEPFILRR 218
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
703-999 8.10e-85

SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.


Pssm-ID: 425504 [Multi-domain]  Cd Length: 289  Bit Score: 279.95  E-value: 8.10e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922   703 YQLEGLNWLRFSWAQ-GTDTILADEMGLGKTVQTIVFLYSLYKEGHSKG-PYLVSAPLSTIINWEREFEMWA--PDFYVV 778
Cdd:pfam00176    1 YQIEGVNWMLSLENNlGRGGILADEMGLGKTLQTISLLLYLKHVDKNWGgPTLIVVPLSLLHNWMNEFERWVspPALRVV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922   779 TYTGDKESRSVIREnefsfednairsgkkvfrmKKEVQIKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQSK 858
Cdd:pfam00176   81 VLHGNKRPQERWKN-------------------DPNFLADFDVVITTYETLRKHKELLKKVHWHRIVLDEGHRLKNSKSK 141
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922   859 FFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEF-ADISKEDQ---IKKLHDLLGPHMLRRLKA 934
Cdd:pfam00176  142 LSKALKSLKTRNRWILTGTPLQNNLEELWALLNFLRPGPFGSLSTFRNWFdRPIERGGGkkgVSRLHKLLKPFLLRRTKK 221
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 119591922   935 DVFKNMPAKTELIVRVELSQMQKKYYK-FILTRNFEALNSKGGGNQV--SLLNIMMDLKKCCNHPYLF 999
Cdd:pfam00176  222 DVEKSLPPKVEYILFCRLSKLQRKLYQtFLLKKDLNAIKTGEGGREIkaSLLNILMRLRKICNHPGLI 289
DEXHc_Snf cd17919
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
700-895 2.83e-82

DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350677 [Multi-domain]  Cd Length: 182  Bit Score: 267.89  E-value: 2.83e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVVT 779
Cdd:cd17919     1 LRPYQLEGLNFLLELYENGPGGILADEMGLGKTLQAIAFLAYLLKEGKERGPVLVVCPLSVLENWEREFEKWTPDLRVVV 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  780 YTGDKESRSVIRenefsfednairsgkkvfrmKKEVQIKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQSKF 859
Cdd:cd17919    81 YHGSQRERAQIR--------------------AKEKLDKFDVVLTTYETLRRDKASLRKFRWDLVVVDEAHRLKNPKSQL 140
                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 119591922  860 FRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTP 895
Cdd:cd17919   141 SKALKALRAKRRLLLTGTPLQNNLEELWALLDFLDP 176
CHDII_SANT-like pfam06461
CHD subfamily II, SANT-like domain; CHD proteins (name derived from the presence of a ...
1389-1529 4.05e-79

CHD subfamily II, SANT-like domain; CHD proteins (name derived from the presence of a Chromodomain, SWI2/SNF2 ATPase/Helicase and a motif with sequence similarity to a DNA)binding domain) are ATP-dependent chromatin remodelers found in plant and animals. In eukaryotes, there are three subfamilies, I, II and III. This domain is found in members of subfamily II which play a role in repression of genes involved in developmental regulation, including Mi-2 from Drosophila melanogaster, CHD3/4/5 from animals and PICKLE (a CHD3/4-related protein) from Arabidopsis. Sequence analysis revealed that this domain has a considerable similarity to SANT domains suggesting that it fold into this type of domain and it is integral to the DNA binding domain of CHD remodelers in subfamily II.


Pssm-ID: 461920  Cd Length: 137  Bit Score: 256.91  E-value: 4.05e-79
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  1389 GQSGRRQSRRQLKSDRDKPLPpLLARVGGNIEVLGFNARQRKAFLNAIMRWGMppqDAFNSHWLVRDLRGKSEKEFRAYV 1468
Cdd:pfam06461    1 PQTGRRPYRRRARVDKDEPLP-LMEGEGGSIEVLGFNARQRKAFLNALMRYGM---GNFDWKEFVRDLRGKTEKEIKAYG 76
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 119591922  1469 SLFMRHLCEPGADGAETFADGVPREGLSRQHVLTRIGVMSLVRKKVQEFEHVNGKYSTPDL 1529
Cdd:pfam06461   77 SLFLRHICEPGADNSETFADGVPKEGLSRQDVLTRIGVMSLIRKKVQEFEHIPGKPSFPDL 137
DEXHc_CHD2 cd18054
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2; ...
684-931 3.00e-78

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2; Chromodomain-helicase-DNA-binding protein 2 (CHD2) is a DNA-binding helicase that specifically binds to the promoter of target genes, leading to chromatin remodeling, possibly by promoting deposition of histone H3.3. It is involved in myogenesis via interaction with MYOD1; it binds to myogenic gene regulatory sequences and mediates incorporation of histone H3.3 prior to the onset of myogenic gene expression, promoting their expression. CHD2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350812 [Multi-domain]  Cd Length: 237  Bit Score: 258.78  E-value: 3.00e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  684 VKFDKQPWYIDSTGGTLHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIIN 763
Cdd:cd18054     5 VALKKQPSYIGGENLELRDYQLEGLNWLAHSWCKNNSVILADEMGLGKTIQTISFLSYLFHQHQLYGPFLLVVPLSTLTS 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  764 WEREFEMWAPDFYVVTYTGDKESRSVIRENEFSFEDNAirsgkkvfrmkkevQIKFHVLLTSYELITIDQAILGSIEWAC 843
Cdd:cd18054    85 WQREFEIWAPEINVVVYIGDLMSRNTIREYEWIHSQTK--------------RLKFNALITTYEILLKDKTVLGSINWAF 150
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  844 LVVDEAHRLKNNQSKFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADiSKEDQIKKLHDL 923
Cdd:cd18054   151 LGVDEAHRLKNDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFEFWEDFEEDHGK-GRENGYQSLHKV 229

                  ....*...
gi 119591922  924 LGPHMLRR 931
Cdd:cd18054   230 LEPFLLRR 237
DEXHc_HELLS_SMARCA6 cd18009
DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or ...
697-933 1.05e-72

DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or SMARCA6) is a major epigenetic regulator crucial for normal heterochromatin structure and function. HELLS is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350767 [Multi-domain]  Cd Length: 236  Bit Score: 243.06  E-value: 1.05e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  697 GGTLHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGhSKGPYLVSAPLSTIINWEREFEMWAPDFY 776
Cdd:cd18009     1 GGVMRPYQLEGMEWLRMLWENGINGILADEMGLGKTIQTIALLAHLRERG-VWGPFLVIAPLSTLPNWVNEFARFTPSVP 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  777 VVTYTGDKESRSVIRENefsfednairsgkkvfRMKKEVQI-KFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNN 855
Cdd:cd18009    80 VLLYHGTKEERERLRKK----------------IMKREGTLqDFPVVVTSYEIAMRDRKALQHYAWKYLIVDEGHRLKNL 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  856 QSKFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFL------------EEFADISKEDQ---IKKL 920
Cdd:cd18009   144 NCRLIQELKTFNSDNRLLLTGTPLQNNLSELWSLLNFLLPDVFDDLSSFEswfdfsslsdnaADISNLSEEREqniVHML 223
                         250
                  ....*....|...
gi 119591922  921 HDLLGPHMLRRLK 933
Cdd:cd18009   224 HAILKPFLLRRLK 236
DEXHc_SMARCA2_SMARCA4 cd17996
DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin ...
697-933 1.99e-71

DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, members 2 and 4 (SMARCA2 and SMARCA4) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350754 [Multi-domain]  Cd Length: 233  Bit Score: 239.19  E-value: 1.99e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  697 GGTLHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFY 776
Cdd:cd17996     1 GGTLKEYQLKGLQWMVSLYNNNLNGILADEMGLGKTIQTISLITYLMEKKKNNGPYLVIVPLSTLSNWVSEFEKWAPSVS 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  777 VVTYTGDKESRsvirenefsfednairsgKKVFrmKKEVQIKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQ 856
Cdd:cd17996    81 KIVYKGTPDVR------------------KKLQ--SQIRAGKFNVLLTTYEYIIKDKPLLSKIKWKYMIIDEGHRMKNAQ 140
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  857 SKFFRVLNS-YKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFA------------DISKEDQ---IKKL 920
Cdd:cd17996   141 SKLTQTLNTyYHARYRLLLTGTPLQNNLPELWALLNFLLPKIFKSCKTFEQWFNtpfantgeqvkiELNEEETlliIRRL 220
                         250
                  ....*....|...
gi 119591922  921 HDLLGPHMLRRLK 933
Cdd:cd17996   221 HKVLRPFLLRRLK 233
DEXHc_CHD6 cd18058
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 6; ...
700-931 2.81e-69

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 6; Chromodomain-helicase-DNA-binding protein 6 (CHD6) is a DNA-dependent ATPase that plays a role in chromatin remodeling. It regulates transcription by disrupting nucleosomes in a largely non-sliding manner which strongly increases the accessibility of chromatin. It activates transcription of specific genes in response to oxidative stress through interaction with NFE2L2.2 and acts as a transcriptional repressor of different viruses including influenza virus or papillomavirus. During influenza virus infection, the viral polymerase complex localizes CHD6 to inactive chromatin where it gets degraded in a proteasome independent-manner. CHD6 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350816 [Multi-domain]  Cd Length: 222  Bit Score: 232.63  E-value: 2.81e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGhSKGPYLVSAPLSTIINWEREFEMWApDFYVVT 779
Cdd:cd18058     1 LREYQLEGMNWLLFNWYNRKNCILADEMGLGKTIQSITFLSEIFLMG-IRGPFLIIAPLSTITNWEREFRTWT-EMNAIV 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  780 YTGDKESRSVIRENEFSFEDNAIRSGKKVFrmkkevqiKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQSKF 859
Cdd:cd18058    79 YHGSQISRQMIQQYEMYYRDEQGNPLSGIF--------KFQVVITTFEMILADCPELKKINWSCVIIDEAHRLKNRNCKL 150
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 119591922  860 FRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISKEDQIKKLHDLLGPHMLRR 931
Cdd:cd18058   151 LEGLKLMALEHKVLLTGTPLQNSVEELFSLLNFLEPSQFPSETTFLEEFGDLKTEEQVKKLQSILKPMMLRR 222
DEXHc_CHD7 cd18059
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 7; ...
700-931 1.21e-66

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 7; Chromodomain-helicase-DNA-binding protein 7 (CHD7) is a probable transcription regulator. It may be involved in the 45S precursor rRNA production. CHD7 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350817 [Multi-domain]  Cd Length: 222  Bit Score: 224.91  E-value: 1.21e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGhSKGPYLVSAPLSTIINWEREFEMWApDFYVVT 779
Cdd:cd18059     1 LREYQLEGVNWLLFNWYNTRNCILADEMGLGKTIQSITFLYEIYLKG-IHGPFLVIAPLSTIPNWEREFRTWT-ELNVVV 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  780 YTGDKESRSVIRENEFSFEDNAIRSGKKVFrmkkevqiKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQSKF 859
Cdd:cd18059    79 YHGSQASRRTIQLYEMYFKDPQGRVIKGSY--------KFHAIITTFEMILTDCPELRNIPWRCVVIDEAHRLKNRNCKL 150
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 119591922  860 FRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISKEDQIKKLHDLLGPHMLRR 931
Cdd:cd18059   151 LEGLKMMDLEHKVLLTGTPLQNTVEELFSLLHFLEPSRFPSETTFMQEFGDLKTEEQVQKLQAILKPMMLRR 222
DEXHc_CHD1L cd18006
DEAH/Q-box helicase domain of CHD1L; Chromodomain helicase DNA binding protein 1 like (CHD1L, ...
700-931 1.72e-66

DEAH/Q-box helicase domain of CHD1L; Chromodomain helicase DNA binding protein 1 like (CHD1L, also known as ALC1) is involved in DNA repair by regulating chromatin relaxation following DNA damage. CHD1L is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350764 [Multi-domain]  Cd Length: 216  Bit Score: 224.24  E-value: 1.72e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVVT 779
Cdd:cd18006     1 LRPYQLEGVNWLLQCRAEQHGCILGDEMGLGKTCQTISLLWYLAGRLKLLGPFLVLCPLSVLDNWKEELNRFAPDLSVIT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  780 YTGDKESRSVIRENEFSFEDnairsgkkvfrmkkevqikFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQSKF 859
Cdd:cd18006    81 YMGDKEKRLDLQQDIKSTNR-------------------FHVLLTTYEICLKDASFLKSFPWASLVVDEAHRLKNQNSLL 141
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 119591922  860 FRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERF--NNLEGFLEEFADISKEDQ-IKKLHDLLGPHMLRR 931
Cdd:cd18006   142 HKTLSEFSVDFRLLLTGTPIQNSLQELYALLSFIEPNVFpkDKLDDFIKAYSETDDESEtVEELHLLLQPFLLRR 216
DEXHc_SMARCA1_SMARCA5 cd17997
DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin ...
697-933 2.58e-66

DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 and 5 (SMARCA1 and SMARCA5) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350755 [Multi-domain]  Cd Length: 222  Bit Score: 224.12  E-value: 2.58e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  697 GGTLHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFY 776
Cdd:cd17997     1 GGTMRDYQIRGLNWLISLFENGINGILADEMGLGKTLQTISLLGYLKHYKNINGPHLIIVPKSTLDNWMREFKRWCPSLR 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  777 VVTYTGDKESRSVIRENEFsfednairsgkkvfrmkkeVQIKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQ 856
Cdd:cd17997    81 VVVLIGDKEERADIIRDVL-------------------LPGKFDVCITSYEMVIKEKTVLKKFNWRYIIIDEAHRIKNEK 141
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  857 SKFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFaDISKEDQ-----IKKLHDLLGPHMLRR 931
Cdd:cd17997   142 SKLSQIVRLFNSRNRLLLTGTPLQNNLHELWALLNFLLPDVFTSSEDFDEWF-NVNNCDDdnqevVQRLHKVLRPFLLRR 220

                  ..
gi 119591922  932 LK 933
Cdd:cd17997   221 IK 222
DEXHc_CHD8 cd18060
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 8; ...
700-931 9.07e-65

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 8; Chromodomain-helicase-DNA-binding protein 8 (CHD8) is a DNA helicase that acts as a chromatin remodeling factor and regulates transcription. It also acts as a transcription repressor by remodeling chromatin structure and recruiting histone H1 to target genes. It suppresses p53/TP53-mediated apoptosis by recruiting histone H1 and preventing p53/TP53 transactivation activity and of STAT3 activity by suppressing the LIF-induced STAT3 transcriptional activity. It also acts as a negative regulator of Wnt signaling pathway and CTNNB1-targeted gene expression. CHD8 is also involved in both enhancer blocking and epigenetic remodeling at chromatin boundary via its interaction with CTCF. It also acts as a transcription activator via its interaction with ZNF143 by participating in efficient U6 RNA polymerase III transcription. CHD8 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350818 [Multi-domain]  Cd Length: 222  Bit Score: 219.54  E-value: 9.07e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGhSKGPYLVSAPLSTIINWEREFEMWApDFYVVT 779
Cdd:cd18060     1 LREYQLEGVNWLLFNWYNRQNCILADEMGLGKTIQSIAFLQEVYNVG-IHGPFLVIAPLSTITNWEREFNTWT-EMNTIV 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  780 YTGDKESRSVIRENEFSFEDNAIRSGKKVFrmkkevqiKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQSKF 859
Cdd:cd18060    79 YHGSLASRQMIQQYEMYCKDSRGRLIPGAY--------KFDALITTFEMILSDCPELREIEWRCVIIDEAHRLKNRNCKL 150
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 119591922  860 FRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISKEDQIKKLHDLLGPHMLRR 931
Cdd:cd18060   151 LDSLKHMDLEHKVLLTGTPLQNTVEELFSLLHFLEPSQFPSESEFLKDFGDLKTEEQVQKLQAILKPMMLRR 222
DEXHc_CHD9 cd18061
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 9; ...
700-931 4.94e-64

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 9; Chromodomain-helicase-DNA-binding protein 9 (CHD9) acts as a transcriptional coactivator for PPARA and possibly other nuclear receptors. It is proposed to be a ATP-dependent chromatin remodeling protein. CHD9 has DNA-dependent ATPase activity and binds to A/T-rich DNA. It also associates with A/T-rich regulatory regions in promoters of genes that participate in the differentiation of progenitors during osteogenesis. CHD9 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350819 [Multi-domain]  Cd Length: 222  Bit Score: 217.57  E-value: 4.94e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGhSKGPYLVSAPLSTIINWEREFEMWApDFYVVT 779
Cdd:cd18061     1 LREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFLYEILLTG-IRGPFLIIAPLSTIANWEREFRTWT-DLNVVV 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  780 YTGDKESRSVIRENEFSFEDNAIRSGKKVFRmkkevqikFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQSKF 859
Cdd:cd18061    79 YHGSLISRQMIQQYEMYFRDSQGRIIRGAYR--------FQAIITTFEMILGGCPELNAIDWRCVIIDEAHRLKNKNCKL 150
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 119591922  860 FRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISKEDQIKKLHDLLGPHMLRR 931
Cdd:cd18061   151 LEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFGDLKTEEQVQKLQAILKPMMLRR 222
DEXHc_CHD1 cd18053
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 1; ...
684-931 3.37e-62

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 1; Chromodomain-helicase-DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. It regulates polymerase II transcription and is also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. It is not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome. CHD1 is also associated with histone deacetylase (HDAC) activity. It is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350811 [Multi-domain]  Cd Length: 237  Bit Score: 212.99  E-value: 3.37e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  684 VKFDKQPWYIDSTGG-TLHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTII 762
Cdd:cd18053     4 VALKKQPSYIGGHEGlELRDYQLNGLNWLAHSWCKGNSCILADEMGLGKTIQTISFLNYLFHEHQLYGPFLLVVPLSTLT 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  763 NWEREFEMWAPDFYVVTYTGDKESRSVIRENEFSFEDNAirsgkkvfrmkkevQIKFHVLLTSYELITIDQAILGSIEWA 842
Cdd:cd18053    84 SWQREIQTWAPQMNAVVYLGDINSRNMIRTHEWMHPQTK--------------RLKFNILLTTYEILLKDKSFLGGLNWA 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  843 CLVVDEAHRLKNNQSKFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADiSKEDQIKKLHD 922
Cdd:cd18053   150 FIGVDEAHRLKNDDSLLYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPEKFSSWEDFEEEHGK-GREYGYASLHK 228

                  ....*....
gi 119591922  923 LLGPHMLRR 931
Cdd:cd18053   229 ELEPFLLRR 237
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
1023-1149 3.81e-60

C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350180 [Multi-domain]  Cd Length: 135  Bit Score: 202.71  E-value: 3.81e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922 1023 SGKLMLLQKMLKKLRDEGHRVLIFSQMTKMLDLLEDFLEYEGYKYERIDGGITGGLRQEAIDRFNAPGaQQFCFLLSTRA 1102
Cdd:cd18793    10 SGKLEALLELLEELREPGEKVLIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFNEDP-DIRVFLLSTKA 88
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 119591922 1103 GGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQNKKVMIYRFV 1149
Cdd:cd18793    89 GGVGLNLTAANRVILYDPWWNPAVEEQAIDRAHRIGQKKPVVVYRLI 135
DEXQc_SRCAP cd18003
DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or ...
700-931 1.08e-58

DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or DOMO1) is the core catalytic component of the multiprotein chromatin-remodeling SRCAP complex, that is necessary for the incorporation of the histone variant H2A.Z into nucleosomes. SRCAP is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350761 [Multi-domain]  Cd Length: 223  Bit Score: 202.20  E-value: 1.08e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVVT 779
Cdd:cd18003     1 LREYQHIGLDWLATLYEKNLNGILADEMGLGKTIQTIALLAHLACEKGNWGPHLIVVPTSVMLNWEMEFKRWCPGFKILT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  780 YTGDKESRSVIRENefSFEDNAirsgkkvfrmkkevqikFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQSKF 859
Cdd:cd18003    81 YYGSAKERKLKRQG--WMKPNS-----------------FHVCITSYQLVVQDHQVFKRKKWKYLILDEAHNIKNFKSQR 141
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  860 FRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFAD----ISKEDQ------IKKLHDLLGPHML 929
Cdd:cd18003   142 WQTLLNFNTQRRLLLTGTPLQNSLMELWSLMHFLMPHIFQSHQEFKEWFSNpltaMSEGSQeeneelVRRLHKVLRPFLL 221

                  ..
gi 119591922  930 RR 931
Cdd:cd18003   222 RR 223
DEXQc_arch_SWI2_SNF2 cd18012
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ...
698-933 1.66e-58

DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging to SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The Snf2 family comprises a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. Archaeal SWI2 and SNF2 are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350770 [Multi-domain]  Cd Length: 218  Bit Score: 201.25  E-value: 1.66e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  698 GTLHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGhSKGPYLVSAPLSTIINWEREFEMWAPDFYV 777
Cdd:cd18012     3 ATLRPYQKEGFNWLSFLRHYGLGGILADDMGLGKTLQTLALLLSRKEEG-RKGPSLVVAPTSLIYNWEEEAAKFAPELKV 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  778 VTYTGDKESRSVIRENEfsfednairsgkkvfrmkkevqiKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQS 857
Cdd:cd18012    82 LVIHGTKRKREKLRALE-----------------------DYDLVITSYGLLRRDIELLKEVKFHYLVLDEAQNIKNPQT 138
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  858 KFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFA-DISK---EDQIKKLHDLLGPHMLRRLK 933
Cdd:cd18012   139 KTAKAVKALKADHRLALTGTPIENHLGELWSIFDFLNPGLLGSYKRFKKRFAkPIEKdgdEEALEELKKLISPFILRRLK 218
DEXQc_INO80 cd18002
DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 ...
700-931 5.43e-55

DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 chromatin remodeling complex. INO80 removes histone H3-containing nucleosomes from associated chromatin, promotes CENP-ACnp1 chromatin assembly at the centromere in a redundant manner with another chromatin-remodeling factor Chd1Hrp1. INO80 mutants have severe defects in oxygen consumption and promiscuous cell division that is no longer coupled with metabolic status. INO80 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350760 [Multi-domain]  Cd Length: 229  Bit Score: 191.95  E-value: 5.43e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVVT 779
Cdd:cd18002     1 LKEYQLKGLNWLANLYEQGINGILADEMGLGKTVQSIAVLAHLAEEHNIWGPFLVIAPASTLHNWQQEISRFVPQFKVLP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  780 YTGDKESRSVIRENefsfednaiRSGKKVFRMKKevqiKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQSKF 859
Cdd:cd18002    81 YWGNPKDRKVLRKF---------WDRKNLYTRDA----PFHVVITSYQLVVQDEKYFQRVKWQYMVLDEAQAIKSSSSSR 147
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  860 FRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFA-DIS---------KEDQIKKLHDLLGPHML 929
Cdd:cd18002   148 WKTLLSFHCRNRLLLTGTPIQNSMAELWALLHFIMPTLFDSHDEFNEWFSkDIEshaenktglNEHQLKRLHMILKPFML 227

                  ..
gi 119591922  930 RR 931
Cdd:cd18002   228 RR 229
DEXHc_SMARCA5 cd18064
DEAH-box helicase domain of SMARCA5; SWI/SNF related, matrix associated, actin dependent ...
685-943 7.13e-52

DEAH-box helicase domain of SMARCA5; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 (SMARCA5, also called SNF2H) is the catalytic subunit of the four known chromatin-remodeling complexes: CHRAC, RSF, ACF/WCRF, and WICH. SMARCA5 plays a major role organising arrays of nucleosomes adjacent to the binding sites for the architectural transcription factor CTCF sites and acts to promote CTCF binding SMARCA5 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350822 [Multi-domain]  Cd Length: 244  Bit Score: 183.33  E-value: 7.13e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  685 KFDKQPWYIdsTGGTLHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINW 764
Cdd:cd18064     3 RFEDSPSYV--KWGKLRDYQVRGLNWLISLYENGINGILADEMGLGKTLQTISLLGYMKHYRNIPGPHMVLVPKSTLHNW 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  765 EREFEMWAPDFYVVTYTGDKESRSvirenefSFEDNAIRSGKkvfrmkkevqikFHVLLTSYELITIDQAILGSIEWACL 844
Cdd:cd18064    81 MAEFKRWVPTLRAVCLIGDKDQRA-------AFVRDVLLPGE------------WDVCVTSYEMLIKEKSVFKKFNWRYL 141
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  845 VVDEAHRLKNNQSKFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFAD---ISKEDQIKKLH 921
Cdd:cd18064   142 VIDEAHRIKNEKSKLSEIVREFKTTNRLLLTGTPLQNNLHELWALLNFLLPDVFNSAEDFDSWFDTnncLGDQKLVERLH 221
                         250       260
                  ....*....|....*....|..
gi 119591922  922 DLLGPHMLRRLKADVFKNMPAK 943
Cdd:cd18064   222 MVLRPFLLRRIKADVEKSLPPK 243
DEXHc_SMARCAD1 cd17998
DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent ...
700-898 8.65e-52

DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 (SMARCAD1, also known as ATP-dependent helicase 1 or Hel1) possesses intrinsic ATP-dependent nucleosome-remodeling activity and is required for both DNA repair and heterochromatin organization. SMARCAD1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350756 [Multi-domain]  Cd Length: 187  Bit Score: 181.04  E-value: 8.65e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHsKGPYLVSAPLSTIINWEREFEMWAPDFYVVT 779
Cdd:cd17998     1 LKDYQLIGLNWLNLLYQKKLSGILADEMGLGKTIQVIAFLAYLKEIGI-PGPHLVVVPSSTLDNWLREFKRWCPSLKVEP 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  780 YTGDKESRSVIRENEfsfednairsgkkvfrmkKEVQIKFHVLLTSYELIT---IDQAILGSIEWACLVVDEAHRLKNNQ 856
Cdd:cd17998    80 YYGSQEERKHLRYDI------------------LKGLEDFDVIVTTYNLATsnpDDRSFFKRLKLNYVVYDEGHMLKNMT 141
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 119591922  857 SKFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERF 898
Cdd:cd17998   142 SERYRHLMTINANFRLLLTGTPLQNNLLELMSLLNFIMPKPF 183
DEXHc_SMARCA1 cd18065
DEAH-box helicase domain of SMARCA1; SWI/SNF related, matrix associated, actin dependent ...
684-933 5.32e-51

DEAH-box helicase domain of SMARCA1; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 (SMARCA1, also called SNF2L) is a component of NURF (nucleosome-remodeling factor) and CERF (CECR2-containing-remodeling factor) complexes which promote the perturbation of chromatin structure in an ATP-dependent manner. SMARCA1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350823 [Multi-domain]  Cd Length: 233  Bit Score: 180.60  E-value: 5.32e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  684 VKFDKQPWYIdsTGGTLHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIIN 763
Cdd:cd18065     2 VRFEESPSYV--KGGTLRDYQVRGLNWMISLYENGVNGILADEMGLGKTLQTIALLGYLKHYRNIPGPHMVLVPKSTLHN 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  764 WEREFEMWAPDFYVVTYTGDKESRSVIRENEFsfednairsgkkvfrMKKEvqikFHVLLTSYELITIDQAILGSIEWAC 843
Cdd:cd18065    80 WMNEFKRWVPSLRAVCLIGDKDARAAFIRDVM---------------MPGE----WDVCVTSYEMVIKEKSVFKKFNWRY 140
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  844 LVVDEAHRLKNNQSKFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFAD---ISKEDQIKKL 920
Cdd:cd18065   141 LVIDEAHRIKNEKSKLSEIVREFKTTNRLLLTGTPLQNNLHELWALLNFLLPDVFNSADDFDSWFDTkncLGDQKLVERL 220
                         250
                  ....*....|...
gi 119591922  921 HDLLGPHMLRRLK 933
Cdd:cd18065   221 HAVLKPFLLRRIK 233
DEXHc_SMARCA2 cd18063
DEXH-box helicase domain of SMARCA2; SWI/SNF related, matrix associated, actin dependent ...
698-933 4.56e-50

DEXH-box helicase domain of SMARCA2; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 (SMARCA2, also known as brahma homolog) is a component of the BAF complex. SMARCA2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350821 [Multi-domain]  Cd Length: 251  Bit Score: 178.72  E-value: 4.56e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  698 GTLHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYV 777
Cdd:cd18063    22 GTLKHYQLQGLEWMVSLYNNNLNGILADEMGLGKTIQTIALITYLMEHKRLNGPYLIIVPLSTLSNWTYEFDKWAPSVVK 101
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  778 VTYTGDKESRSVIRENefsfednaIRSGkkvfrmkkevqiKFHVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQS 857
Cdd:cd18063   102 ISYKGTPAMRRSLVPQ--------LRSG------------KFNVLLTTYEYIIKDKHILAKIRWKYMIVDEGHRMKNHHC 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  858 KFFRVLNS-YKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEF----------ADISKEDQ---IKKLHDL 923
Cdd:cd18063   162 KLTQVLNThYVAPRRILLTGTPLQNKLPELWALLNFLLPTIFKSCSTFEQWFnapfamtgerVDLNEEETiliIRRLHKV 241
                         250
                  ....*....|
gi 119591922  924 LGPHMLRRLK 933
Cdd:cd18063   242 LRPFLLRRLK 251
DEXHc_SMARCA4 cd18062
DEXH-box helicase domain of SMARCA4; SWI/SNF related, matrix associated, actin dependent ...
683-933 6.47e-49

DEXH-box helicase domain of SMARCA4; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 (SMARCA4, also known as transcription activator BRG1) is a component of the CREST-BRG1 complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. Mutation of SMARCA4 (BRG1), the ATPase of BAF (mSWI/SNF) and PBAF complexes, contributes to a range of malignancies and neurologic disorders. SMARCA4 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350820 [Multi-domain]  Cd Length: 251  Bit Score: 175.23  E-value: 6.47e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  683 TVKFDKQPWYIdsTGGTLHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTII 762
Cdd:cd18062     9 TEKVEKQSSLL--VNGVLKQYQIKGLEWLVSLYNNNLNGILADEMGLGKTIQTIALITYLMEHKRINGPFLIIVPLSTLS 86
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  763 NWEREFEMWAPDFYVVTYTGDKESRSVIREnefsfednAIRSGkkvfrmkkevqiKFHVLLTSYELITIDQAILGSIEWA 842
Cdd:cd18062    87 NWVYEFDKWAPSVVKVSYKGSPAARRAFVP--------QLRSG------------KFNVLLTTYEYIIKDKQILAKIRWK 146
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  843 CLVVDEAHRLKNNQSKFFRVLNS-YKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEF----------ADI 911
Cdd:cd18062   147 YMIVDEGHRMKNHHCKLTQVLNThYVAPRRLLLTGTPLQNKLPELWALLNFLLPTIFKSCSTFEQWFnapfamtgekVDL 226
                         250       260
                  ....*....|....*....|....*
gi 119591922  912 SKEDQ---IKKLHDLLGPHMLRRLK 933
Cdd:cd18062   227 NEEETiliIRRLHKVLRPFLLRRLK 251
DEXHc_ERCC6L2 cd18005
DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as ...
700-931 7.17e-43

DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as RAD26L) may play a role in DNA repair and mitochondrial function. In humans, mutations in the ERCC6L2 gene are associated with bone marrow failure syndrome 2. ERCC6L2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350763 [Multi-domain]  Cd Length: 245  Bit Score: 157.54  E-value: 7.17e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLY-----------------KEGHS---KGPYLVSAPLS 759
Cdd:cd18005     1 LRDYQREGVEFMYDLYKNGRGGILGDDMGLGKTVQVIAFLAAVLgktgtrrdrennrprfkKKPPAssaKKPVLIVAPLS 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  760 TIINWEREFEMWApDFYVVTYTGdkesrsvirenefsfednairSGKKVFRMKKEVQIKFHVLLTSYELITIDQAILGSI 839
Cdd:cd18005    81 VLYNWKDELDTWG-HFEVGVYHG---------------------SRKDDELEGRLKAGRLEVVVTTYDTLRRCIDSLNSI 138
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  840 EWACLVVDEAHRLKNNQSKFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFAD--------- 910
Cdd:cd18005   139 NWSAVIADEAHRIKNPKSKLTQAMKELKCKVRIGLTGTLLQNNMKELWCLLDWAVPGALGSRSQFKKHFSEpikrgqrht 218
                         250       260
                  ....*....|....*....|....*..
gi 119591922  911 -----ISKEDQIKK-LHDLLGPHMLRR 931
Cdd:cd18005   219 atareLRLGRKRKQeLAVKLSKFFLRR 245
DEXHc_ERCC6 cd18000
DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, ...
700-895 1.58e-41

DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, also known Cockayne syndrome group B (CSB), Rad26 in Saccharomyces cerevisiae, and Rhp26 in Schizosaccharomyces pombe) is a DNA-binding protein that is important in transcription-coupled excision repair. ERCC6 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350758 [Multi-domain]  Cd Length: 193  Bit Score: 151.71  E-value: 1.58e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFyvvt 779
Cdd:cd18000     1 LFKYQQTGVQWLWELHCQRVGGILGDEMGLGKTIQIIAFLAALHHSKLGLGPSLIVCPATVLKQWVKEFHRWWPPF---- 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  780 ytgdkesRSVIRENEFSFeDNAIRSGKKVFRMKKEVQIKF---HVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQ 856
Cdd:cd18000    77 -------RVVVLHSSGSG-TGSEEKLGSIERKSQLIRKVVgdgGILITTYEGFRKHKDLLLNHNWQYVILDEGHKIRNPD 148
                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 119591922  857 SKFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTP 895
Cdd:cd18000   149 AEITLACKQLRTPHRLILSGTPIQNNLKELWSLFDFVFP 187
CD1_tandem_CHD3-4_like cd18667
repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and ...
465-544 2.30e-39

repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, and similar proteins; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD3 and CHD4. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. Human CHD3 (also named Mi-2 alpha) and CHD4 (also named Mi-2 beta) are coexpressed in many cell lines and tissues and may act as the motor subunit of the NuRD complex (nucleosome remodeling and deacetylase activities). The proteins form distinct CHD3- and CHD4-NuRD complexes that repress, as well as activate gene transcription of overlapping and specific target genes. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349314 [Multi-domain]  Cd Length: 79  Bit Score: 140.94  E-value: 2.30e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  465 LKGKVQRILHWRWTEPPAPfMVGLPGPDVEPSLPPPKPLEGIPEREFFVKWAGLSYWHCSWVKELQLELYHTVMYRNYQR 544
Cdd:cd18667     1 LKGKVEKILTWRWAEPPYP-EPLPEKPDEDPYPPPPRKLQPRPEREFFVKWHGMSYWHCEWVSELQLEVHHPAMYRNYQR 79
DEXHc_ATRX-like cd18007
DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as ...
700-908 6.93e-39

DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as transcriptional regulator ATRX (also called alpha thalassemia/mental retardation syndrome X-linked and X-linked nuclear protein or XNP) which is involved in transcriptional regulation and chromatin remodeling, and ARIP4 (also called androgen receptor-interacting protein 4, RAD54 like 2 or RAD54L2) which modulates androgen receptor (AR)-dependent transactivation in a promoter-dependent manner. They are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350765 [Multi-domain]  Cd Length: 239  Bit Score: 145.90  E-value: 6.93e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLnwlRFSWAQ--GTDT--------ILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFE 769
Cdd:cd18007     1 LKPHQVEGV---RFLWSNlvGTDVgsdegggcILAHTMGLGKTLQVITFLHTYLAAAPRRSRPLVLCPASTLYNWEDEFK 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  770 MWAPDFYVVTYTGDkesrsvirenefsfEDNAIRSGKKVFRMKKevqiKFH----VLLTSYEL--------ITIDQAILG 837
Cdd:cd18007    78 KWLPPDLRPLLVLV--------------SLSASKRADARLRKIN----KWHkeggVLLIGYELfrnlasnaTTDPRLKQE 139
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 119591922  838 SIEWAC------LVVDEAHRLKNNQSKFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEF 908
Cdd:cd18007   140 FIAALLdpgpdlLVLDEGHRLKNEKSQLSKALSKVKTKRRILLTGTPLQNNLKEYWTMVDFARPKYLGTLKEFKKKF 216
DEXHc_RAD54 cd18004
DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are ...
700-931 2.56e-37

DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350762 [Multi-domain]  Cd Length: 240  Bit Score: 141.27  E-value: 2.56e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWL-----RFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGP----YLVSAPLSTIINWEREFEM 770
Cdd:cd18004     1 LRPHQREGVQFLydcltGRRGYGGGGAILADEMGLGKTLQAIALVWTLLKQGPYGKPtakkALIVCPSSLVGNWKAEFDK 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  771 WAPDFYVVTYTGDKESRSVIRENEFSFEDNAirsgkkvfrmkkevqikFHVLLTSYELITIDQAILGS-IEWACLVVDEA 849
Cdd:cd18004    81 WLGLRRIKVVTADGNAKDVKASLDFFSSAST-----------------YPVLIISYETLRRHAEKLSKkISIDLLICDEG 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  850 HRLKNNQSKFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEF---------ADISKEDQI--- 917
Cdd:cd18004   144 HRLKNSESKTTKALNSLPCRRRLLLTGTPIQNDLDEFFALVDFVNPGILGSLASFRKVFeepilrsrdPDASEEDKElga 223
                         250
                  ....*....|....*..
gi 119591922  918 KKLHDL---LGPHMLRR 931
Cdd:cd18004   224 ERSQELselTSRFILRR 240
DEXDc_SHPRH-like cd18008
DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the ...
700-931 2.98e-37

DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350766 [Multi-domain]  Cd Length: 241  Bit Score: 141.27  E-value: 2.98e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWLRFswaQGTdtILADEMGLGKTVQTIVFLYS------------LYKEGHSKGPY-----LVSAPLSTII 762
Cdd:cd18008     1 LLPYQKQGLAWMLP---RGG--ILADEMGLGKTIQALALILAtrpqdpkipeelEENSSDPKKLYlskttLIVVPLSLLS 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  763 NWEREFEM--WAPDFYVVTYTGDKESRSvirenefsfednairsgkkvfrmkKEVQIKFHVLLTSYELITID-------- 832
Cdd:cd18008    76 QWKDEIEKhtKPGSLKVYVYHGSKRIKS------------------------IEELSDYDIVITTYGTLASEfpknkkgg 131
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  833 --------QAILGSIEWACLVVDEAHRLKNNQSKFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGF 904
Cdd:cd18008   132 grdskekeASPLHRIRWYRVILDEAHNIKNRSTKTSRAVCALKAERRWCLTGTPIQNSLDDLYSLLRFLRVEPFGDYPWF 211
                         250       260       270
                  ....*....|....*....|....*....|
gi 119591922  905 LEEFADISKEDQ---IKKLHDLLGPHMLRR 931
Cdd:cd18008   212 NSDISKPFSKNDrkaLERLQALLKPILLRR 241
DEXHc_Mot1 cd17999
DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in ...
700-931 1.04e-36

DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in eukaryotes) regulates transcription in association with TATA binding protein (TBP). Mot1, Ino80C, and NC2 function coordinately to regulate pervasive transcription in yeast and mammals. Mot1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350757 [Multi-domain]  Cd Length: 232  Bit Score: 139.41  E-value: 1.04e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYS-------LYKEGHSkgPYLVSAPLSTIINWEREFEMWA 772
Cdd:cd17999     1 LRPYQQEGINWLAFLNKYNLHGILCDDMGLGKTLQTLCILASdhhkranSFNSENL--PSLVVCPPTLVGHWVAEIKKYF 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  773 PDFY--VVTYTGDKESRSVIREnefsfednairsgkkvfrmkkevQIKFH-VLLTSYELITIDQAILGSIEWACLVVDEA 849
Cdd:cd17999    79 PNAFlkPLAYVGPPQERRRLRE-----------------------QGEKHnVIVASYDVLRNDIEVLTKIEWNYCVLDEG 135
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  850 HRLKNNQSKFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFA----------DISKEDQ--- 916
Cdd:cd17999   136 HIIKNSKTKLSKAVKQLKANHRLILSGTPIQNNVLELWSLFDFLMPGYLGTEKQFQRRFLkpilasrdskASAKEQEaga 215
                         250
                  ....*....|....*..
gi 119591922  917 --IKKLHDLLGPHMLRR 931
Cdd:cd17999   216 laLEALHKQVLPFLLRR 232
DEXHc_ERCC6L cd18001
DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint ...
700-931 7.46e-36

DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint helicase (ERCC6L, also known as RAD26L) is an essential component of the mitotic spindle assembly checkpoint, by acting as a tension sensor that associates with catenated DNA which is stretched under tension until it is resolved during anaphase. ERCC6L is proposed to stimulate cancer cell proliferation by promoting cell cycle through a way of RAB31-MAPK-CDK2. ERCC6L is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350759 [Multi-domain]  Cd Length: 232  Bit Score: 136.73  E-value: 7.46e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKGPyLVSAPLSTIINWEREFEMWAPDFYVVT 779
Cdd:cd18001     1 LYPHQREGVAWLWSLHDGGKGGILADDMGLGKTVQICAFLSGMFDSGLIKSV-LVVMPTSLIPHWVKEFAKWTPGLRVKV 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  780 YTGdkesrSVIRENEFSFEdnairsgkkvfrmkkEVQIKFHVLLTSYELITIDQAILGSIE-----WACLVVDEAHRLKN 854
Cdd:cd18001    80 FHG-----TSKKERERNLE---------------RIQRGGGVLLTTYGMVLSNTEQLSADDhdefkWDYVILDEGHKIKN 139
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  855 NQSKFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPerfNNLEGFLEEF----------ADISKEDQIKK----- 919
Cdd:cd18001   140 SKTKSAKSLREIPAKNRIILTGTPIQNNLKELWALFDFACN---GSLLGTRKTFkmefenpitrGRDKDATQGEKalgse 216
                         250
                  ....*....|....*.
gi 119591922  920 ----LHDLLGPHMLRR 931
Cdd:cd18001   217 vaenLRQIIKPYFLRR 232
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
1024-1138 5.14e-31

Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 118.47  E-value: 5.14e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  1024 GKLMLLQKMLKKLRdeGHRVLIFSQMTKMLDLlEDFLEYEGYKYERIDGGITGGLRQEAIDRFNAPgaqQFCFLLSTRAG 1103
Cdd:pfam00271    1 EKLEALLELLKKER--GGKVLIFSQTKKTLEA-ELLLEKEGIKVARLHGDLSQEEREEILEDFRKG---KIDVLVATDVA 74
                           90       100       110
                   ....*....|....*....|....*....|....*
gi 119591922  1104 GLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIG 1138
Cdd:pfam00271   75 ERGLDLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
345-387 1.88e-30

PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the first PHD finger.


Pssm-ID: 277006 [Multi-domain]  Cd Length: 43  Bit Score: 114.62  E-value: 1.88e-30
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  345 YCEVCQQGGEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15531     1 YCEVCQQGGEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 43
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
418-460 7.70e-29

PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the second PHD finger.


Pssm-ID: 277007 [Multi-domain]  Cd Length: 43  Bit Score: 110.06  E-value: 7.70e-29
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  418 FCRVCKDGGELLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15532     1 FCRVCKDGGELLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43
DEXHc_RAD54A cd18067
DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as ...
700-931 2.46e-27

DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as RAD54L or RAD54, plays a role in homologous recombination related repair of DNA double-strand breaks. RAD54A is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350825 [Multi-domain]  Cd Length: 243  Bit Score: 112.56  E-value: 2.46e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLnwlRFSWAQGTDT--------ILADEMGLGKTVQTIVFLYSLYKEGHSKGPYL----VSAPLSTIINWERE 767
Cdd:cd18067     1 LRPHQREGV---KFLYRCVTGRrirgshgcIMADEMGLGKTLQCITLMWTLLRQSPQCKPEIdkaiVVSPSSLVKNWANE 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  768 FEMW-APDFYVVTYTGdKESRSVIRENEFSFEDNAIRSGKKVfrmkkevqikfhvLLTSYELITIDQAILGSIEWACLVV 846
Cdd:cd18067    78 LGKWlGGRLQPLAIDG-GSKKEIDRKLVQWASQQGRRVSTPV-------------LIISYETFRLHVEVLQKGEVGLVIC 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  847 DEAHRLKNNQSKFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEF---------ADISK---- 913
Cdd:cd18067   144 DEGHRLKNSDNQTYQALDSLNTQRRVLLSGTPIQNDLSEYFSLVNFVNPGILGTAAEFKKNFelpilkgrdADASEkerq 223
                         250       260
                  ....*....|....*....|
gi 119591922  914 --EDQIKKLHDLLGPHMLRR 931
Cdd:cd18067   224 lgEEKLQELISIVNRCIIRR 243
DEXHc_RAD54B cd18066
DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as ...
700-895 5.75e-26

DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as RDH54, binds to double-stranded DNA, displays ATPase activity in the presence of DNA, and may have a role in meiotic and mitotic recombination. RAD54B is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350824 [Multi-domain]  Cd Length: 235  Bit Score: 108.39  E-value: 5.75e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWL-------RFSWAQGTdtILADEMGLGKTVQTIVFLYSLYKEGHSKGP-----YLVSAPLSTIINWERE 767
Cdd:cd18066     1 LRPHQREGIEFLyecvmgmRVNERFGA--ILADEMGLGKTLQCISLIWTLLRQGPYGGKpvikrALIVTPGSLVKNWKKE 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  768 FEMW--APDFYVVTYTGDKESRSVIRENEFSfednairsgkkvfrmkkevqikfhVLLTSYELITIDQAILGSIEWACLV 845
Cdd:cd18066    79 FQKWlgSERIKVFTVDQDHKVEEFIASPLYS------------------------VLIISYEMLLRSLDQISKLNFDLVI 134
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 119591922  846 VDEAHRLKNNQSKFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTP 895
Cdd:cd18066   135 CDEGHRLKNTSIKTTTALTSLSCERRIILTGTPIQNDLQEFFALIDFVNP 184
DEXHc_HARP_SMARCAL1 cd18010
DEXH-box helicase domain of SMARCAL1; SMARCAL1 (SWI/SNF related, matrix associated, actin ...
700-931 9.50e-26

DEXH-box helicase domain of SMARCAL1; SMARCAL1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1, also known as HARP) is recruited to stalled replication forks to promote repair and helps restart replication. It plays a role in DNA repair, telomere maintenance and replication fork stability in response to DNA replication stress. Mutations cause Schimke Immunoosseous Dysplasia. SMARCAL1 is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350768 [Multi-domain]  Cd Length: 213  Bit Score: 106.91  E-value: 9.50e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLnwlRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGhskgPYLVSAPLSTIINWEREFEMWAPDfyvvt 779
Cdd:cd18010     1 LLPFQREGV---CFALRRGGRVLIADEMGLGKTVQAIAIAAYYREEW----PLLIVCPSSLRLTWADEIERWLPS----- 68
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  780 ytgdkesrsvirenEFSFEDNAIRSGKKVFRMKkevQIKfhVLLTSYELITIDQAILGSIEWACLVVDEAHRLKNNQSKF 859
Cdd:cd18010    69 --------------LPPDDIQVIVKSKDGLRDG---DAK--VVIVSYDLLRRLEKQLLARKFKVVICDESHYLKNSKAKR 129
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  860 FRVLNSY--KIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLE---------GFLEEFADISKEDQIKKLHDLLGPH- 927
Cdd:cd18010   130 TKAALPLlkRAKRVILLSGTPALSRPIELFTQLDALDPKLFGRFHdfgrrycaaKQGGFGWDYSGSSNLEELHLLLLATi 209

                  ....
gi 119591922  928 MLRR 931
Cdd:cd18010   210 MIRR 213
CD2_tandem_CHD3-4_like cd18662
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and ...
589-642 1.23e-25

repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, and similar proteins; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD3 and CHD4, and yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. Human CHD3 (also named Mi-2 alpha) and CHD4 (also named Mi-2 beta) are coexpressed in many cell lines and tissues and may act as the motor subunit of the NuRD complex (nucleosome remodeling and deacetylase activities). The proteins form distinct CHD3- and CHD4-NuRD complexes that repress, as well as activate gene transcription of overlapping and specific target genes. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349309 [Multi-domain]  Cd Length: 55  Bit Score: 101.19  E-value: 1.23e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 119591922  589 PEWMMIHRILNHSFDKKGDVHYLIKWKDLPYDQCTWEIDDIDIPYYDNLKQAYW 642
Cdd:cd18662     1 PEWLQIHRIINHRVDKDGNTWYLVKWRDLPYDQSTWESEDDDIPDYEKHIQEYW 54
DEXDc smart00487
DEAD-like helicases superfamily;
694-902 1.37e-24

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 103.34  E-value: 1.37e-24
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922    694 DSTGGTLHPYQLEGLNWLRFSWaqgTDTILADEMGLGKTVQTIVFLYSLYKEGhSKGPYLVSAPL-STIINWEREFEMWA 772
Cdd:smart00487    3 KFGFEPLRPYQKEAIEALLSGL---RDVILAAPTGSGKTLAALLPALEALKRG-KGGRVLVLVPTrELAEQWAEELKKLG 78
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922    773 PDFY--VVTYTGDKESRSVIREnefsfednaIRSGkkvfrmkkevqiKFHVLLTSYELIT--IDQAILGSIEWACLVVDE 848
Cdd:smart00487   79 PSLGlkVVGLYGGDSKREQLRK---------LESG------------KTDILVTTPGRLLdlLENDKLSLSNVDLVILDE 137
                           170       180       190       200       210       220
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 119591922    849 AHRLKNNqsKFFRVLNSY-----KIDYKLLLTGTP---LQNNLEELFHLLNFLTPERFNNLE 902
Cdd:smart00487  138 AHRLLDG--GFGDQLEKLlkllpKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPLEP 197
HELICc smart00490
helicase superfamily c-terminal domain;
1054-1138 3.84e-24

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 97.67  E-value: 3.84e-24
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922   1054 DLLEDFLEYEGYKYERIDGGITGGLRQEAIDRFNAPgaqQFCFLLSTRAGGLGINLATADTVIIYDSDWNPHNDIQAFSR 1133
Cdd:smart00490    1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNG---KIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGR 77

                    ....*
gi 119591922   1134 AHRIG 1138
Cdd:smart00490   78 AGRAG 82
CHDNT pfam08073
CHDNT (NUC034) domain; The CHDNT domain is found in PHD/RING finger and chromo ...
145-200 1.51e-23

CHDNT (NUC034) domain; The CHDNT domain is found in PHD/RING finger and chromo domain-associated helicases.


Pssm-ID: 462357  Cd Length: 54  Bit Score: 95.09  E-value: 1.51e-23
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 119591922   145 DVDYlfSEEDYHTLTNYKAFSQFLRPLIAKKNPKIPMSKMMTVLGAKWREFSANNP 200
Cdd:pfam08073    1 EIDY--DEEDFQNLTTYKLFSQHVRPLLLKANPKVPMSKMMMLVAAKWREFQNHNP 54
DEXDc_RapA cd18011
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ...
700-931 6.32e-23

DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350769 [Multi-domain]  Cd Length: 207  Bit Score: 98.90  E-value: 6.32e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNW------LRFswaqgtdtILADEMGLGKTVQTIVFLYSLYKEGHSKgPYLVSAPLSTIINWEreFEMW-- 771
Cdd:cd18011     1 PLPHQIDAVLRalrkppVRL--------LLADEVGLGKTIEAGLIIKELLLRGDAK-RVLILCPASLVEQWQ--DELQdk 69
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  772 -APDFYVVtytgDKESRSVIRenefsfednaiRSGKKVFRMkkevqikFHVLLTSYELI---TIDQAILGSIEWACLVVD 847
Cdd:cd18011    70 fGLPFLIL----DRETAAQLR-----------RLIGNPFEE-------FPIVIVSLDLLkrsEERRGLLLSEEWDLVVVD 127
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  848 EAHRLKNNQ----SKFFRVLN--SYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEfadiskedqiKKLH 921
Cdd:cd18011   128 EAHKLRNSGggkeTKRYKLGRllAKRARHVLLLTATPHNGKEEDFRALLSLLDPGRFAVLGRFLRL----------DGLR 197
                         250
                  ....*....|
gi 119591922  922 DLLGPHMLRR 931
Cdd:cd18011   198 EVLAKVLLRR 207
DEXHc_ARIP4 cd18069
DEXH-box helicase domain of ARIP4; Androgen receptor-interacting protein 4 (ARIP4, also called ...
700-908 1.60e-22

DEXH-box helicase domain of ARIP4; Androgen receptor-interacting protein 4 (ARIP4, also called RAD54 like 2 or RAD54L2 ) modulates androgen receptor (AR)-dependent transactivation in a promoter-dependent manner. ARIP4 is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350827 [Multi-domain]  Cd Length: 227  Bit Score: 98.35  E-value: 1.60e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWL---------RFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKgPYLVSAPLSTIINWEREFEM 770
Cdd:cd18069     1 LKPHQIGGIRFLydniiesleRYKGSSGFGCILAHSMGLGKTLQVISFLDVLLRHTGAK-TVLAIVPVNTLQNWLSEFNK 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  771 WAPDFyvvtytgdkESRSVIRENefSFEDNAIRSGKKVFRMKKEVQIKFH----VLLTSYELITIDQAIlgsiewACLVV 846
Cdd:cd18069    80 WLPPP---------EALPNVRPR--PFKVFILNDEHKTTAARAKVIEDWVkdggVLLMGYEMFRLRPGP------DVVIC 142
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 119591922  847 DEAHRLKNNQSKFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEF 908
Cdd:cd18069   143 DEGHRIKNCHASTSQALKNIRSRRRIVLTGYPLQNNLIEYWCMVDFVRPDFLGTRQEFSNMF 204
DEXHc_HLTF1_SMARC3 cd18071
DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as ...
722-905 1.36e-21

DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as HIP116 or SMARCA3) has both helicase and E3 ubiquitin ligase activities and ATP-dependent nucleosome-remodeling activity. HLTF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350829 [Multi-domain]  Cd Length: 239  Bit Score: 96.00  E-value: 1.36e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  722 ILADEMGLGKTVQTIVFLYSlykeghskGPYLVSAPLSTIINWEREFEMW----APDFYvvTYTGDKESRSVireNEFSF 797
Cdd:cd18071    52 ILADDMGLGKTLTTISLILA--------NFTLIVCPLSVLSNWETQFEEHvkpgQLKVY--TYHGGERNRDP---KLLSK 118
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  798 EDnairsgkkvfrmkkevqikfhVLLTSYELITIDQAI-----LGSIEWACLVVDEAHRLKNNQSKFFRVLNSYKIDYKL 872
Cdd:cd18071   119 YD---------------------IVLTTYNTLASDFGAkgdspLHTINWLRVVLDEGHQIRNPNAQQTKAVLNLSSERRW 177
                         170       180       190
                  ....*....|....*....|....*....|...
gi 119591922  873 LLTGTPLQNNLEELFHLLNFLTPERFNNLEGFL 905
Cdd:cd18071   178 VLTGTPIQNSPKDLGSLLSFLHLKPFSNPEYWR 210
DEXHc_ATRX cd18068
DEXH-box helicase domain of ATRX; Transcriptional regulator ATRX (also called alpha ...
700-910 1.98e-21

DEXH-box helicase domain of ATRX; Transcriptional regulator ATRX (also called alpha thalassemia/mental retardation syndrome X-linked and X-linked nuclear protein or XNP) is involved in transcriptional regulation and chromatin remodeling. Mutations in humans cause mental retardation, X-linked, syndromic, with hypotonic facies 1 (MRXSHF1) and alpha-thalassemia myelodysplasia syndrome (ATMDS). ATRX is part of the a DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350826 [Multi-domain]  Cd Length: 246  Bit Score: 95.73  E-value: 1.98e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLnwlRFSW------------AQGTDTILADEMGLGKTVQTIVFLYSLY----KEGHSKGpyLVSAPLSTIIN 763
Cdd:cd18068     1 LKPHQVDGV---QFMWdccceslkktkkSPGSGCILAHCMGLGKTLQVVTFLHTVLlcekLENFSRV--LVVCPLNTVLN 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  764 WEREFEMWAP--------DFYVVTYTGDKESRSvIRENEFSFEDNAIRSGKKVFR-MKKEVQIKfhvllTSYELITIDQA 834
Cdd:cd18068    76 WLNEFEKWQEglkdeekiEVNELATYKRPQERS-YKLQRWQEEGGVMIIGYDMYRiLAQERNVK-----SREKLKEIFNK 149
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 119591922  835 ILGSIEWACLVVDEAHRLKNNQSKFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPerfnNLEGFLEEFAD 910
Cdd:cd18068   150 ALVDPGPDFVVCDEGHILKNEASAVSKAMNSIRTKRRIVLTGTPLQNNLIEYHCMVNFVKP----NLLGTIKEFRN 221
PHD1_PHF12 cd15533
PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is ...
419-460 2.13e-21

PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. PHF12 contains two plant-homeodomain (PHD) zinc fingers followed by a polybasic region. The PHD fingers function downstream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides. This model corresponds to the first PHD finger.


Pssm-ID: 277008 [Multi-domain]  Cd Length: 45  Bit Score: 88.57  E-value: 2.13e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 119591922  419 CRVCKDGGELLCCDACPSSYHLHCLNPPLPE--IPNGEWLCPRC 460
Cdd:cd15533     2 CDSCGEGGDLLCCDRCPASFHLQCCNPPLDEedLPPGEWLCHRC 45
DUF1087 pfam06465
CHD subfamily II, DUF1087; This domain is found in chromatin remodelling factors (CHDs) from ...
1298-1351 2.27e-21

CHD subfamily II, DUF1087; This domain is found in chromatin remodelling factors (CHDs) from subfamily II including CHD3/4/5 from animals and PICKLE. from Arabidopsis. The exact function is, as yet, unknown.


Pssm-ID: 461922  Cd Length: 60  Bit Score: 89.02  E-value: 2.27e-21
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 119591922  1298 EDGVEEVEREIIKQE-ENVDPDYWEKLLRHHYEQQQEDLARNLGKGKRIRKQVNY 1351
Cdd:pfam06465    1 AAAEEEAQKEVIKEEnESEDPNYWEKLLKHHYEQQQEEEFNALGKGKRSRKQVVS 55
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
418-460 1.39e-18

PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC complex protein BHC80) along with HDAC1/2, CtBP1, CoREST, and BRAF35, is associated with LSD1, a lysine (K)-specific histone demethylase. It inhibits LSD1-mediated histone demethylation in vitro. PHF21A is predominantly present in the central nervous system and spermatogenic cells and is one of the six components of BRAF-HDAC complex (BHC) involved in REST-dependent transcriptional repression of neuron-specific genes in non-neuronal cells. It acts as a scaffold protein in BHC in neuronal as well as non-neuronal cells and also plays a role in spermatogenesis. PHF21A contains a C-terminal plant homeodomain (PHD) finger that is responsible for the binding directly to each of five other components of BHC, and of organizing BHC mediating transcriptional repression.


Pssm-ID: 276998 [Multi-domain]  Cd Length: 43  Bit Score: 80.52  E-value: 1.39e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  418 FCRVCKDGGELLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15523     1 FCSVCRKSGELLMCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
345-387 2.21e-18

PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the second PHD finger.


Pssm-ID: 277007 [Multi-domain]  Cd Length: 43  Bit Score: 80.02  E-value: 2.21e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  345 YCEVCQQGGEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15532     1 FCRVCKDGGELLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
419-460 5.51e-18

PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) protein, functions as a regulator of gene transcription in the thymus. It is essential for prevention of autoimmunity. AIRE plays a critical role in the induction of central tolerance. It promotes self-tolerance through tissue-specific antigen (TSA) expression. It also acts as an active regulator of chondrocyte differentiation. AIRE contains a homogeneously-staining region (HSR) or caspase-recruitment domain (CARD), a nuclear localization signal (NLS), a SAND (for Sp100, AIRE, nuclear phosphoprotein 41/75 or NucP41/75, and deformed epidermal auto regulatory factor 1 or Deaf1) domain, two plant homeodomain (PHD) fingers, and four LXXLL (where L stands for leucine) motifs. This model corresponds to the first PHD finger that recognizes the unmethylated tail of histone H3 and targets AIRE-dependent genes.


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 79.03  E-value: 5.51e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 119591922  419 CRVCKDGGELLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15539     2 CAVCGDGGELLCCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
418-460 8.18e-18

PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar proteins; The TIF1 family of transcriptional cofactors includes TIF1alpha (TRIM24), TIF1beta (TRIM28), TIF1gamma (TRIM33), and TIF1delta (TRIM66), which are characterized by an N-terminal RING-finger B-box coiled-coil (RBCC/TRIM) motif and plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha, TIF1beta, and TIF1delta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. TIF1alpha and TIF1beta bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. In contrast, TIF1delta appears to lack nuclear receptor- and KRAB-binding activity. Moreover, TIF1delta is specifically involved in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta, and gamma. It cannot bind to nuclear receptors (NRs). This family also includes Sp100/Sp140 family proteins, the nuclear body SP100 and SP140. Sp110 is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. SP140 is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus viral infectivity factor (Vif) protein. Both Sp110 and Sp140 contain a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD).


Pssm-ID: 277016 [Multi-domain]  Cd Length: 43  Bit Score: 78.54  E-value: 8.18e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  418 FCRVCKDGGELLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15541     1 WCAVCQNGGELLCCDKCPRVFHLDCHIPPIPEFPSGEWSCSLC 43
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
418-462 2.94e-17

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 77.15  E-value: 2.94e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 119591922   418 FCRVCK---DGGELLCCDACPSSYHLHCLNPPLP--EIPNGEWLCPRCTC 462
Cdd:pfam00628    1 YCAVCGksdDGGELVQCDGCDDWFHLACLGPPLDpaEIPSGEWLCPECKP 50
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
345-387 1.47e-16

PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) protein, functions as a regulator of gene transcription in the thymus. It is essential for prevention of autoimmunity. AIRE plays a critical role in the induction of central tolerance. It promotes self-tolerance through tissue-specific antigen (TSA) expression. It also acts as an active regulator of chondrocyte differentiation. AIRE contains a homogeneously-staining region (HSR) or caspase-recruitment domain (CARD), a nuclear localization signal (NLS), a SAND (for Sp100, AIRE, nuclear phosphoprotein 41/75 or NucP41/75, and deformed epidermal auto regulatory factor 1 or Deaf1) domain, two plant homeodomain (PHD) fingers, and four LXXLL (where L stands for leucine) motifs. This model corresponds to the first PHD finger that recognizes the unmethylated tail of histone H3 and targets AIRE-dependent genes.


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 74.79  E-value: 1.47e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  345 YCEVCQQGGEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15539     1 ECAVCGDGGELLCCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
345-387 1.93e-16

PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC complex protein BHC80) along with HDAC1/2, CtBP1, CoREST, and BRAF35, is associated with LSD1, a lysine (K)-specific histone demethylase. It inhibits LSD1-mediated histone demethylation in vitro. PHF21A is predominantly present in the central nervous system and spermatogenic cells and is one of the six components of BRAF-HDAC complex (BHC) involved in REST-dependent transcriptional repression of neuron-specific genes in non-neuronal cells. It acts as a scaffold protein in BHC in neuronal as well as non-neuronal cells and also plays a role in spermatogenesis. PHF21A contains a C-terminal plant homeodomain (PHD) finger that is responsible for the binding directly to each of five other components of BHC, and of organizing BHC mediating transcriptional repression.


Pssm-ID: 276998 [Multi-domain]  Cd Length: 43  Bit Score: 74.74  E-value: 1.93e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  345 YCEVCQQGGEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15523     1 FCSVCRKSGELLMCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43
PHD1_BPTF cd15559
PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, ...
419-460 2.21e-16

PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, also termed nucleosome-remodeling factor subunit BPTF, or fetal Alz-50 clone 1 protein (FAC1), or fetal Alzheimer antigen, functions as a transcriptional regulator that exhibits altered expression and subcellular localization during neuronal development and neurodegenerative diseases such as Alzheimer's disease. It interacts with the human orthologue of the Kelch-like Ech-associated protein (Keap1). Its function and subcellular localization can be regulated by Keap1. Moreover, BPTF is a novel DNA-binding protein that recognizes the DNA sequence CACAACAC and represses transcription through this site in a phosphorylation-dependent manner. Furthermore, BPTF interacts with the Myc-associated zinc finger protein (ZF87/MAZ) and alters its transcriptional activity, which has been implicated in gene regulation in neurodegeneration. Some family members contain two or three plant homeodomain (PHD) fingers, which may be involved in complex formation with histone H3 trimethylated at K4 (H3K4me3). This family corresponds to the first PHD finger.


Pssm-ID: 277034 [Multi-domain]  Cd Length: 43  Bit Score: 74.37  E-value: 2.21e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 119591922  419 CRVCKDGGELLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15559     2 CRVCHKLGDLLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43
CD2_tandem cd18659
repeat 2 of paired tandem chromodomains; Repeat 2 of tandem CHRomatin Organization Modifier ...
590-642 2.49e-16

repeat 2 of paired tandem chromodomains; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 to CHD9, and yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349306 [Multi-domain]  Cd Length: 54  Bit Score: 74.53  E-value: 2.49e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 119591922  590 EWMMIHRILNHSFDKKGDVHYLIKWKDLPYDQCTWEIDDIDIPYYDNLKQAYW 642
Cdd:cd18659     1 EYTIVERIIAHREDDEGVTEYLVKWKGLPYDECTWESEEDISDIFQEAIDEYK 53
CD1_tandem cd18660
repeat 1 of paired tandem chromodomains; Repeat 1 of tandem CHRomatin Organization Modifier ...
466-544 5.20e-16

repeat 1 of paired tandem chromodomains; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 to CHD9, and yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349307 [Multi-domain]  Cd Length: 70  Bit Score: 74.32  E-value: 5.20e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  466 KGKVQRILHWRWTEPPAPFMVGLPGPDVEPslpppkplegiPEREFFVKWAGLSYWHCSWVKELQLELYHT-VMYRNYQR 544
Cdd:cd18660     2 EDKIEKILDHRPKGPVEEASLDLTDPDEPW-----------DEREFLVKWKGKSYLHCTWVTEETLEQLRGkKKLKNYIK 70
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
419-460 5.29e-16

PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins; Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model corresponds to the first PHD finger.


Pssm-ID: 276994 [Multi-domain]  Cd Length: 46  Bit Score: 73.27  E-value: 5.29e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  419 CRVC---KDGGELLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15519     2 CEVCgldDNEGEVLLCDGCDAEYHTSCLDPPLGEIPPGTWFCPSC 46
PHD_PHF21B cd15524
PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) ...
345-387 3.07e-15

PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) finger-containing protein whose biological function remains unclear. It shows high sequence similarity with PHF21A, which is associated with LSD1, a lysine (K)-specific histone demethylase and inhibits LSD1-mediated histone demethylation in vitro. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.


Pssm-ID: 276999 [Multi-domain]  Cd Length: 43  Bit Score: 71.08  E-value: 3.07e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  345 YCEVCQQGGEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15524     1 HCAACKRGGNLQPCGTCPRAYHLDCLDPPLKTAPKGVWVCPKC 43
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
418-460 3.69e-15

PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the first PHD finger.


Pssm-ID: 277006 [Multi-domain]  Cd Length: 43  Bit Score: 71.09  E-value: 3.69e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  418 FCRVCKDGGELLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15531     1 YCEVCQQGGEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 43
PHD1_Rco1 cd15535
PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and ...
418-460 4.10e-15

PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and similar proteins; Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two plant homeodomain (PHD) fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the first PHD finger.


Pssm-ID: 277010 [Multi-domain]  Cd Length: 45  Bit Score: 70.91  E-value: 4.10e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  418 FCRVCKDGGELLCCDACPSSYHLHCLNPPLPE--IPNGEWLCPRC 460
Cdd:cd15535     1 FCSACGGYGSFLCCDGCPRSFHFSCLDPPLEEdnLPDDEWFCNEC 45
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
345-387 5.22e-15

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 70.60  E-value: 5.22e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 119591922   345 YCEVCQQ---GGEIILCDTCPRAYHLVCLDPELEKA--PEGKWSCPHC 387
Cdd:pfam00628    1 YCAVCGKsddGGELVQCDGCDDWFHLACLGPPLDPAeiPSGEWLCPEC 48
DEXHc_TTF2 cd18072
DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called ...
700-931 5.55e-15

DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called Forkhead-box E1/FOXE1 ) is a transcription termination factor that couples ATP hydrolysis with the removal of RNA polymerase II from the DNA template. Single nucleotide polymorphism (SNP) within the 5'-UTR of TTF2 is associated with thyroid cancer risk.TTF2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350830 [Multi-domain]  Cd Length: 241  Bit Score: 76.75  E-value: 5.55e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWLRFSWAQG-TDTILADEMGLGKTVQTI-VFLYSLYKEGHSKGP---------------------YLVSA 756
Cdd:cd18072     1 LLLHQKQALAWLLWRERQKpRGGILADDMGLGKTLTMIaLILAQKNTQNRKEEEkekalteweskkdstlvpsagTLVVC 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  757 PLSTIINWEREFEmwapdfyvvtytgDKESRSVIRENEFSfEDNAIRSGKkVFRmkkevqiKFHVLLTSYELI------- 829
Cdd:cd18072    81 PASLVHQWKNEVE-------------SRVASNKLRVCLYH-GPNRERIGE-VLR-------DYDIVITTYSLVakeipty 138
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  830 --TIDQAILGSIEWACLVVDEAHRLKNNQSKFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEE 907
Cdd:cd18072   139 keESRSSPLFRIAWARIILDEAHNIKNPKVQASIAVCKLRAHARWALTGTPIQNNLLDMYSLLKFLRCSPFDDLKVWKKQ 218
                         250       260
                  ....*....|....*....|....
gi 119591922  908 FADISKEDQiKKLHDLLGPHMLRR 931
Cdd:cd18072   219 VDNKSRKGG-ERLNILTKSLLLRR 241
PHD_PHF21B cd15524
PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) ...
418-460 6.44e-15

PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) finger-containing protein whose biological function remains unclear. It shows high sequence similarity with PHF21A, which is associated with LSD1, a lysine (K)-specific histone demethylase and inhibits LSD1-mediated histone demethylation in vitro. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.


Pssm-ID: 276999 [Multi-domain]  Cd Length: 43  Bit Score: 70.31  E-value: 6.44e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  418 FCRVCKDGGELLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15524     1 HCAACKRGGNLQPCGTCPRAYHLDCLDPPLKTAPKGVWVCPKC 43
PHD1_KDM5A_like cd15515
PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar ...
419-460 7.23e-15

PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar proteins; The JARID subfamily within the JmjC proteins includes Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog, protein little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me2 and H3K4me3), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. This family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent H3K4me3 demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two or three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 276990  Cd Length: 46  Bit Score: 70.11  E-value: 7.23e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  419 CRVCKDGGE---LLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15515     2 CQVCGRGDDedkLLLCDGCDDSYHTFCLIPPLPDIPPGDWRCPKC 46
PHD4_NSD cd15567
PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
418-460 1.40e-14

PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fourth PHD finger.


Pssm-ID: 277042 [Multi-domain]  Cd Length: 41  Bit Score: 69.20  E-value: 1.40e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  418 FCRVCKDGGELLCCDACPSSYHLHCLNppLPEIPNGEWLCPRC 460
Cdd:cd15567     1 WCFICSEGGSLICCESCPASFHPECLG--LEPPPEGKFYCEDC 41
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
418-460 2.55e-14

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 68.78  E-value: 2.55e-14
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 119591922    418 FCRVCK---DGGELLCCDACPSSYHLHCLNPPL-PEIPNGEWLCPRC 460
Cdd:smart00249    1 YCSVCGkpdDGGELLQCDGCDRWYHQTCLGPPLlEEEPDGKWYCPKC 47
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
346-387 2.59e-14

PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins; Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model corresponds to the first PHD finger.


Pssm-ID: 276994 [Multi-domain]  Cd Length: 46  Bit Score: 68.65  E-value: 2.59e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  346 CEVC---QQGGEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15519     2 CEVCgldDNEGEVLLCDGCDAEYHTSCLDPPLGEIPPGTWFCPSC 46
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
345-387 3.63e-14

PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar proteins; The TIF1 family of transcriptional cofactors includes TIF1alpha (TRIM24), TIF1beta (TRIM28), TIF1gamma (TRIM33), and TIF1delta (TRIM66), which are characterized by an N-terminal RING-finger B-box coiled-coil (RBCC/TRIM) motif and plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha, TIF1beta, and TIF1delta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. TIF1alpha and TIF1beta bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. In contrast, TIF1delta appears to lack nuclear receptor- and KRAB-binding activity. Moreover, TIF1delta is specifically involved in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta, and gamma. It cannot bind to nuclear receptors (NRs). This family also includes Sp100/Sp140 family proteins, the nuclear body SP100 and SP140. Sp110 is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. SP140 is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus viral infectivity factor (Vif) protein. Both Sp110 and Sp140 contain a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD).


Pssm-ID: 277016 [Multi-domain]  Cd Length: 43  Bit Score: 68.14  E-value: 3.63e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  345 YCEVCQQGGEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15541     1 WCAVCQNGGELLCCDKCPRVFHLDCHIPPIPEFPSGEWSCSLC 43
PHD1_Lid_like cd15605
PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar ...
419-460 5.09e-14

PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar proteins; Drosophila melanogaster Lid, also termed Retinoblastoma-binding protein 2 homolog, is identified genetically as a trithorax group (trxG) protein that is a Drosophila homolog of the human protein JARID1A/kdm5A, a member of the JARID subfamily within the JmjC proteins. Lid functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Lid contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger of Lid.


Pssm-ID: 277078  Cd Length: 46  Bit Score: 67.86  E-value: 5.09e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  419 CRVCKDG-GE--LLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15605     2 CHTCGRGdGEesMLLCDGCDDSYHTFCLLPPLSEVPKGDWRCPKC 46
PHD4_NSD cd15567
PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
345-387 1.16e-13

PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fourth PHD finger.


Pssm-ID: 277042 [Multi-domain]  Cd Length: 41  Bit Score: 66.50  E-value: 1.16e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  345 YCEVCQQGGEIILCDTCPRAYHLVCLDpeLEKAPEGKWSCPHC 387
Cdd:cd15567     1 WCFICSEGGSLICCESCPASFHPECLG--LEPPPEGKFYCEDC 41
PHD1_PHF12 cd15533
PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is ...
345-387 1.19e-13

PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. PHF12 contains two plant-homeodomain (PHD) zinc fingers followed by a polybasic region. The PHD fingers function downstream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides. This model corresponds to the first PHD finger.


Pssm-ID: 277008 [Multi-domain]  Cd Length: 45  Bit Score: 66.61  E-value: 1.19e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  345 YCEVCQQGGEIILCDTCPRAYHLVCLDP--ELEKAPEGKWSCPHC 387
Cdd:cd15533     1 YCDSCGEGGDLLCCDRCPASFHLQCCNPplDEEDLPPGEWLCHRC 45
PHD1_KDM5C_5D cd15604
PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
419-460 1.39e-13

PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family includes KDM5C and KDM5D, both of which belong to the JARID subfamily within the JmjC proteins. KDM5C (also termed Histone demethylase JARID1C, Jumonji/ARID domain-containing protein 1C, SmcX, or Xe169) is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D (also termed Histocompatibility Y antigen (H-Y), Histone demethylase JARID1D, Jumonji/ARID domain-containing protein 1D, or SmcY) is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 andH3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. Both KDM5C and KDM5D contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277077  Cd Length: 46  Bit Score: 66.40  E-value: 1.39e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  419 CRVCKDGGE---LLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15604     2 CRMCSRGDEddkLLLCDGCDDNYHTFCLLPPLPEPPKGIWRCPKC 46
PHD_TIF1delta cd15625
PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also ...
417-460 1.69e-13

PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also termed tripartite motif-containing protein 66 (TRIM66), is a novel heterochromatin protein 1 (HP1)-interacting member of the transcriptional intermediary factor1 (TIF1) family expressed by elongating spermatids. Like other TIF1 proteins, TIF1delta displays a potent trichostatin A (TSA)-sensitive repression function; TSA is a specific inhibitor of histone deacetylases. Moreover, TIF1delta plays an important role in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. It functions as a negative regulator of postmeiotic genes acting through HP1 isotype gamma (HP1gamma) complex formation and centromere association. TIF1delta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.


Pssm-ID: 277095 [Multi-domain]  Cd Length: 49  Bit Score: 66.52  E-value: 1.69e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 119591922  417 EFCRVCKDGGELLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15625     3 DFCAVCLNGGELLCCDRCPKVFHLSCHVPALLSFPVGEWVCTLC 46
PHD1_Rco1 cd15535
PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and ...
345-387 1.86e-13

PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and similar proteins; Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two plant homeodomain (PHD) fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the first PHD finger.


Pssm-ID: 277010 [Multi-domain]  Cd Length: 45  Bit Score: 66.29  E-value: 1.86e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  345 YCEVCQQGGEIILCDTCPRAYHLVCLDPELEK--APEGKWSCPHC 387
Cdd:cd15535     1 FCSACGGYGSFLCCDGCPRSFHFSCLDPPLEEdnLPDDEWFCNEC 45
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
345-387 2.43e-13

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 66.08  E-value: 2.43e-13
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 119591922    345 YCEVCQQ---GGEIILCDTCPRAYHLVCLDPELEKA-PEGKWSCPHC 387
Cdd:smart00249    1 YCSVCGKpddGGELLQCDGCDRWYHQTCLGPPLLEEePDGKWYCPKC 47
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
694-1164 4.74e-13

Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 74.29  E-value: 4.74e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  694 DSTGGTLHPYQLEGLNWLRFSWAQGTDTILAdEM--GLGKTVqTIVFLYSLYKEGhskGPYLVSAPLSTIIN-WEREFEM 770
Cdd:COG1061    75 SGTSFELRPYQQEALEALLAALERGGGRGLV-VAptGTGKTV-LALALAAELLRG---KRVLVLVPRRELLEqWAEELRR 149
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  771 WAPDFYVVtytgdkesrsvirenefsfednairSGKKvfrmkkevQIKFHVLLTSYELITIDQAI--LGSiEWACLVVDE 848
Cdd:COG1061   150 FLGDPLAG-------------------------GGKK--------DSDAPITVATYQSLARRAHLdeLGD-RFGLVIIDE 195
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  849 AHRLKNNQskFFRVLNSYKIDYKLLLTGTPlqnnleelfhllnfltpERFNNLEGFLEEFADISKEdqiKKLHDLLGPHM 928
Cdd:COG1061   196 AHHAGAPS--YRRILEAFPAAYRLGLTATP-----------------FRSDGREILLFLFDGIVYE---YSLKEAIEDGY 253
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  929 LRrlKADVFknmpaktelIVRVELSQMQKKYYKFIlTRNFEALNSKgggnqvsllnimmdlkkccnhpylfpvaaveapv 1008
Cdd:COG1061   254 LA--PPEYY---------GIRVDLTDERAEYDALS-ERLREALAAD---------------------------------- 287
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922 1009 lpngsydgsslvkSSGKLMLLQKMLKKLRDeGHRVLIFSQMTKMLDLLEDFLEYEGYKYERIDGGITGGLRQEAIDRFNA 1088
Cdd:COG1061   288 -------------AERKDKILRELLREHPD-DRKTLVFCSSVDHAEALAELLNEAGIRAAVVTGDTPKKEREEILEAFRD 353
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922 1089 pGAQQfcFLLSTRAGGLGINLATADTVIIYDsdwnPHND----IQAFSRAHRIGQNKK-VMIYRFVTRASveERITQVAK 1163
Cdd:COG1061   354 -GELR--ILVTVDVLNEGVDVPRLDVAILLR----PTGSprefIQRLGRGLRPAPGKEdALVYDFVGNDV--PVLEELAK 424

                  .
gi 119591922 1164 R 1164
Cdd:COG1061   425 D 425
PHD_TIF1alpha cd15622
PHD finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also ...
418-460 5.90e-13

PHD finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also termed tripartite motif-containing protein 24 (TRIM24), or E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the TRIM/RBCC protein family. It interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoid X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta) and MOD2 (HP1gamma), as well as vertebrate Kruppel-type (C2H2) zinc finger proteins that contain transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of retinoic acid receptor (RAR) that interacts with multiple nuclear receptors in vitro via an LXXLL motif, and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53 and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal plant homeodomain (PHD)-Bromodomain (Bromo) region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development. TIF1-alpha contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.


Pssm-ID: 277092  Cd Length: 43  Bit Score: 64.70  E-value: 5.90e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  418 FCRVCKDGGELLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15622     1 WCAVCQNGGELLCCEKCPKVFHLSCHVPTLMNFPSGEWICTFC 43
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
419-460 1.05e-12

PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1A contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277097 [Multi-domain]  Cd Length: 46  Bit Score: 63.95  E-value: 1.05e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  419 CRVCKDGGE---LLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15627     2 CRICRRKGDaekMLLCDGCDRGHHMYCLRPPLKKVPEGDWFCPDC 46
PHD5_NSD cd15568
PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
345-386 2.05e-12

PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fifth PHD finger.


Pssm-ID: 277043 [Multi-domain]  Cd Length: 43  Bit Score: 63.12  E-value: 2.05e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 119591922  345 YCEVCQQGGEIILCD--TCPRAYHLVCLDpeLEKAPEGKWSCPH 386
Cdd:cd15568     1 ECFRCGDGGDLVLCDfkGCPKVYHLSCLG--LEKPPGGKWICPW 42
PHD_BS69 cd15537
PHD finger found in protein BS69; Protein BS69, also termed zinc finger MYND domain-containing ...
345-387 2.09e-12

PHD finger found in protein BS69; Protein BS69, also termed zinc finger MYND domain-containing protein 11 (ZMYND11 or ZMY11), is a ubiquitously expressed nuclear protein acting as a transcriptional co-repressor in association with various transcription factors. It was originally identified as an adenovirus 5 E1A-binding protein that inhibits E1A transactivation, as well as c-Myb transcription. It also mediates repression, at least in part, through interaction with the co-repressor N-CoR. Moreover, it interacts with Toll-interleukin 1 receptor domain (TIR)-containing adaptor molecule-1 (TICAM-1, also named TRIF) to facilitate NF-kappaB activation and type I IFN induction. It associates with PIAS1, a SUMO E3 enzyme, and Ubc9, a SUMO E2 enzyme, and plays an inhibitory role in muscle and neuronal differentiation. Moreover, BS69 regulates Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1)/C-terminal activation region 2 (CTAR2)-mediated NF-kappaB activation by interfering with the complex formation between TNFR-associated death domain protein (TRADD) and LMP1/CTAR2. It also cooperates with tumor necrosis factor receptor (TNFR)-associated factor 3 (TRAF3) in the regulation of EBV-derived LMP1/CTAR1-induced NF-kappaB activation. Furthermore, BS69 is involved in the p53-p21Cip1-mediated senescence pathway. BS69 contains a plant homeodomain (PHD) finger, a bromodomain, a proline-tryptophan-tryptophan-proline (PWWP) domain, and a Myeloid translocation protein 8, Nervy and DEAF-1 (MYND) domain.


Pssm-ID: 277012  Cd Length: 43  Bit Score: 63.13  E-value: 2.09e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  345 YCEVCQQGGEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15537     1 YCFECHAPGEVLPCSGCFRVYHSDCLSEDFRPDSTSHWTCPVC 43
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
419-460 2.63e-12

PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV pX-associated protein 8, or Hepatitis B virus X-associated protein alpha (HBxAPalpha), or p325 subunit of RSF chromatin-remodeling complex, is a novel nuclear protein with histone chaperon function. It is a subunit of an ISWI chromatin remodeling complex, remodeling and spacing factor (RSF), and plays a role in mediating ATPase-dependent chromatin remodeling and conferring tumor aggressiveness in common carcinomas. As an ataxia-telangiectasia mutated (ATM)-dependent chromatin remodeler, Rsf-1 facilitates DNA damage checkpoints and homologous recombination repair. It regulates the mitotic spindle checkpoint and chromosome instability through the association with serine/threonine kinase BubR1 (BubR1) and Hepatitis B virus (HBV) X protein (HBx) in the chromatin fraction during mitosis. It also interacts with cyclin E1 and promotes tumor development. Rsf-1 contains a plant homeodomain (PHD) finger.


Pssm-ID: 277018 [Multi-domain]  Cd Length: 46  Bit Score: 63.06  E-value: 2.63e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  419 CRVCK---DGGELLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15543     2 CRKCGlsdHPEWILLCDRCDAGYHTACLRPPLMIIPDGNWFCPPC 46
PHD_BAZ1B cd15628
PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also ...
419-460 2.96e-12

PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. BAZ1B contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277098  Cd Length: 46  Bit Score: 62.84  E-value: 2.96e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  419 CRVCKDGGE---LLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15628     2 CKVCRKKGEddkLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
345-387 3.67e-12

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 62.72  E-value: 3.67e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 119591922  345 YCEVCQQGG----EIILCDTCPRAYHLVCLDPELEKA-PEGKWSCPHC 387
Cdd:cd15489     1 SCIVCGKGGdlggELLQCDGCGKWFHADCLGPPLSSFvPNGKWICPVC 48
PHD4_NSD3 cd15658
PHD finger 4 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed ...
418-460 4.49e-12

PHD finger 4 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed histone-lysine N-methyltransferase NSD3, or protein whistle, or WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, or Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1-like protein 1, or WHSC1L1), is a lysine methyltransferase encoded by gene NSD3, which is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD3 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, five plant-homeodomain (PHD) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fourth PHD finger.


Pssm-ID: 277128  Cd Length: 40  Bit Score: 62.24  E-value: 4.49e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  418 FCRVCKDGGELLCCDACPSSYHLHCLNPPLPEipnGEWLCPRC 460
Cdd:cd15658     1 FCFVCARGGRLLCCESCPASFHPECLSIEMPE---GCWNCNEC 40
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
418-460 5.48e-12

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 61.95  E-value: 5.48e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 119591922  418 FCRVCKDGG----ELLCCDACPSSYHLHCLNPPLPE-IPNGEWLCPRC 460
Cdd:cd15489     1 SCIVCGKGGdlggELLQCDGCGKWFHADCLGPPLSSfVPNGKWICPVC 48
PHD1_BPTF cd15559
PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, ...
345-387 6.29e-12

PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, also termed nucleosome-remodeling factor subunit BPTF, or fetal Alz-50 clone 1 protein (FAC1), or fetal Alzheimer antigen, functions as a transcriptional regulator that exhibits altered expression and subcellular localization during neuronal development and neurodegenerative diseases such as Alzheimer's disease. It interacts with the human orthologue of the Kelch-like Ech-associated protein (Keap1). Its function and subcellular localization can be regulated by Keap1. Moreover, BPTF is a novel DNA-binding protein that recognizes the DNA sequence CACAACAC and represses transcription through this site in a phosphorylation-dependent manner. Furthermore, BPTF interacts with the Myc-associated zinc finger protein (ZF87/MAZ) and alters its transcriptional activity, which has been implicated in gene regulation in neurodegeneration. Some family members contain two or three plant homeodomain (PHD) fingers, which may be involved in complex formation with histone H3 trimethylated at K4 (H3K4me3). This family corresponds to the first PHD finger.


Pssm-ID: 277034 [Multi-domain]  Cd Length: 43  Bit Score: 61.66  E-value: 6.29e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  345 YCEVCQQGGEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15559     1 HCRVCHKLGDLLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
419-460 6.93e-12

PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, also termed histone acetyltransferase KAT6A, YBF2/SAS3, SAS2 and TIP60 protein 3 (MYST-3), or runt-related transcription factor-binding protein 2, or zinc finger protein 220, is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF), also termed MOZ2, or histone acetyltransferase KAT6B, or MOZ, YBF2/SAS3, SAS2 and TIP60 protein 4 (MYST4), is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are also implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphomagenesis and bone development, and its homologs. MOZ contains a linker histone 1 and histone 5 domains and two plant homeodomain (PHD) fingers. In contrast, MORF contains an N-terminal region containing two PHD fingers, a putative HAT domain, an acidic region, and a C-terminal Ser/Met-rich domain. The family corresponds to the first PHD finger.


Pssm-ID: 277002  Cd Length: 46  Bit Score: 61.62  E-value: 6.93e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  419 CRVCKDGGE---LLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15527     2 CSVCQDSGNadnLLFCDACDKGFHMECHDPPLTRMPKGKWVCQIC 46
PHD_TIF1gamma cd15624
PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also ...
418-460 7.97e-12

PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also termed tripartite motif-containing 33 (trim33), or ectodermin, or RFG7, or PTC7, is an E3-ubiquitin ligase that functions as a regulator of transforming growth factor beta (TGFbeta) signaling; it inhibits the Smad4-mediated TGFbeta response by interaction with Smad2/3 or ubiquitylation of Smad4. Moreover, TIF1gamma is an important regulator of transcription during hematopoiesis, as well as a key factor of tumorigenesis. Like other TIF1 family members, TIF1gamma also contains an intrinsic transcriptional silencing function. It can control erythroid cell fate by regulating transcription elongation. It can bind to the anaphase-promoting complex/cyclosome (APC/C) and promotes mitosis. TIF1gamma contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.


Pssm-ID: 277094  Cd Length: 46  Bit Score: 61.60  E-value: 7.97e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  418 FCRVCKDGGELLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15624     1 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 43
PHD1_KDM5A cd15602
PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
419-460 1.01e-11

PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2)) was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as a trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277075  Cd Length: 49  Bit Score: 61.50  E-value: 1.01e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  419 CRVCKDGG---ELLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15602     2 CLFCGRGNnedKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKC 46
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
346-387 1.43e-11

PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1A contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277097 [Multi-domain]  Cd Length: 46  Bit Score: 60.87  E-value: 1.43e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  346 CEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15627     2 CRICRRKGDaekMLLCDGCDRGHHMYCLRPPLKKVPEGDWFCPDC 46
PHD5_NSD cd15568
PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
418-459 1.43e-11

PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fifth PHD finger.


Pssm-ID: 277043 [Multi-domain]  Cd Length: 43  Bit Score: 60.81  E-value: 1.43e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 119591922  418 FCRVCKDGGELLCCDA--CPSSYHLHCLNppLPEIPNGEWLCPR 459
Cdd:cd15568     1 ECFRCGDGGDLVLCDFkgCPKVYHLSCLG--LEKPPGGKWICPW 42
PHD_BAZ2A_like cd15545
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B ...
418-460 1.51e-11

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B (BAZ2B); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A. Both BAZ2A and BAZ2B contain a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain. BAZ2B also harbors an extra Apolipophorin-III like domain in its N-terminal region.


Pssm-ID: 277020 [Multi-domain]  Cd Length: 46  Bit Score: 60.79  E-value: 1.51e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 119591922  418 FCRVCKDG---GELLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15545     1 SCQICRSGdneDQLLLCDGCDRGYHTYCFKPKMTNVPEGDWFCPEC 46
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
346-387 1.97e-11

PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, also termed histone acetyltransferase KAT6A, YBF2/SAS3, SAS2 and TIP60 protein 3 (MYST-3), or runt-related transcription factor-binding protein 2, or zinc finger protein 220, is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF), also termed MOZ2, or histone acetyltransferase KAT6B, or MOZ, YBF2/SAS3, SAS2 and TIP60 protein 4 (MYST4), is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are also implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphomagenesis and bone development, and its homologs. MOZ contains a linker histone 1 and histone 5 domains and two plant homeodomain (PHD) fingers. In contrast, MORF contains an N-terminal region containing two PHD fingers, a putative HAT domain, an acidic region, and a C-terminal Ser/Met-rich domain. The family corresponds to the first PHD finger.


Pssm-ID: 277002  Cd Length: 46  Bit Score: 60.47  E-value: 1.97e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  346 CEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15527     2 CSVCQDSGNadnLLFCDACDKGFHMECHDPPLTRMPKGKWVCQIC 46
PHD5_NSD3 cd15661
PHD finger 5 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed ...
345-385 2.19e-11

PHD finger 5 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed histone-lysine N-methyltransferase NSD3, or protein whistle, or WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, or Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1-like protein 1, or WHSC1L1), is a lysine methyltransferase encoded by gene NSD3, which is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD3 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, five plant-homeodomain (PHD) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fifth PHD finger.


Pssm-ID: 277131  Cd Length: 43  Bit Score: 60.37  E-value: 2.19e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  345 YCEVCQQGGEIILCDT--CPRAYHLVCLDpeLEKAPEGKWSCP 385
Cdd:cd15661     1 YCFQCGDGGELVMCDKkdCPKAYHLLCLN--LTQPPYGKWECP 41
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
419-460 2.61e-11

PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. Both BAZ1A and BAZ1B contain a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277019  Cd Length: 46  Bit Score: 60.12  E-value: 2.61e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  419 CRVCK---DGGELLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15544     2 CKVCRkkgDPDNMILCDGCDKAFHLYCLRPALREVPSGDWFCPAC 46
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
419-460 3.41e-11

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277000  Cd Length: 47  Bit Score: 59.69  E-value: 3.41e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 119591922  419 CRVC---KDGGELLCCDACPSSYHLHCLNPPLPEIPNG-EWLCPRC 460
Cdd:cd15525     2 CHVCggkQDPEKQLLCDECDMAYHLYCLDPPLTSLPDDdEWYCPDC 47
PHD_PRKCBP1 cd15538
PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed ...
345-387 4.51e-11

PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), or Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor; the RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a plant homeodomain (PHD) finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277013  Cd Length: 41  Bit Score: 59.26  E-value: 4.51e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  345 YCEVCQQGGEIILCDTCPRAYHLVCLdpELEKAPEGKWSCPHC 387
Cdd:cd15538     1 FCWRCHKEGQVLCCSLCPRVYHKKCL--KLTSEPDEDWVCPEC 41
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
419-460 4.94e-11

PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis antigen 31 (CT31), Histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A)) is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of pregnant females and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277076  Cd Length: 46  Bit Score: 59.19  E-value: 4.94e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  419 CRVCKDGGE---LLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15603     2 CLVCGSGNDedrLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 46
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
346-387 6.04e-11

PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. Both BAZ1A and BAZ1B contain a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277019  Cd Length: 46  Bit Score: 58.96  E-value: 6.04e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  346 CEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15544     2 CKVCRKKGDpdnMILCDGCDKAFHLYCLRPALREVPSGDWFCPAC 46
Chromo pfam00385
Chromo (CHRromatin organization MOdifier) domain;
592-630 7.70e-11

Chromo (CHRromatin organization MOdifier) domain;


Pssm-ID: 459793 [Multi-domain]  Cd Length: 52  Bit Score: 58.74  E-value: 7.70e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 119591922   592 MMIHRILNHSFDKKGDVHYLIKWKDLPYDQCTWE-IDDID 630
Cdd:pfam00385    1 YEVERILDHRKDKGGKEEYLVKWKGYPYDENTWEpEENLS 40
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
419-460 9.54e-11

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2 (also termed Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2) was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs,p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277089  Cd Length: 47  Bit Score: 58.43  E-value: 9.54e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 119591922  419 CRVC---KDGGELLCCDACPSSYHLHCLNPPLPEIPNGE-WLCPRC 460
Cdd:cd15617     2 CYVCggkQDAHMQLLCDECNMAYHIYCLNPPLDKIPEDEdWYCPSC 47
PHD_TIF1alpha cd15622
PHD finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also ...
345-387 1.20e-10

PHD finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also termed tripartite motif-containing protein 24 (TRIM24), or E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the TRIM/RBCC protein family. It interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoid X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta) and MOD2 (HP1gamma), as well as vertebrate Kruppel-type (C2H2) zinc finger proteins that contain transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of retinoic acid receptor (RAR) that interacts with multiple nuclear receptors in vitro via an LXXLL motif, and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53 and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal plant homeodomain (PHD)-Bromodomain (Bromo) region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development. TIF1-alpha contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.


Pssm-ID: 277092  Cd Length: 43  Bit Score: 58.15  E-value: 1.20e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  345 YCEVCQQGGEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15622     1 WCAVCQNGGELLCCEKCPKVFHLSCHVPTLMNFPSGEWICTFC 43
PHD_PHRF1 cd15536
PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also ...
418-460 1.33e-10

PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also termed KIAA1542, or CTD-binding SR-like protein rA9, is a ubiquitin ligase that induces the ubiquitination of TGIF (TG-interacting factor) at lysine 130. It acts as a tumor suppressor that promotes the transforming growth factor (TGF)-beta cytostatic program through selective release of TGIF-driven promyelocytic leukemia protein (PML) inactivation. PHRF1 contains a plant homeodomain (PHD) finger and a RING finger.


Pssm-ID: 277011  Cd Length: 46  Bit Score: 58.19  E-value: 1.33e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 119591922  418 FCRVCKDGGE---LLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15536     1 YCEVCGRSDRedrLLLCDGCDAGYHMECLTPPLDEVPIEEWFCPEC 46
PHD_BAZ1B cd15628
PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also ...
346-387 1.47e-10

PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. BAZ1B contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277098  Cd Length: 46  Bit Score: 57.83  E-value: 1.47e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  346 CEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15628     2 CKVCRKKGEddkLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46
PHD_TIF1delta cd15625
PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also ...
342-387 1.89e-10

PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also termed tripartite motif-containing protein 66 (TRIM66), is a novel heterochromatin protein 1 (HP1)-interacting member of the transcriptional intermediary factor1 (TIF1) family expressed by elongating spermatids. Like other TIF1 proteins, TIF1delta displays a potent trichostatin A (TSA)-sensitive repression function; TSA is a specific inhibitor of histone deacetylases. Moreover, TIF1delta plays an important role in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. It functions as a negative regulator of postmeiotic genes acting through HP1 isotype gamma (HP1gamma) complex formation and centromere association. TIF1delta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.


Pssm-ID: 277095 [Multi-domain]  Cd Length: 49  Bit Score: 57.66  E-value: 1.89e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 119591922  342 HQDYCEVCQQGGEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15625     1 NEDFCAVCLNGGELLCCDRCPKVFHLSCHVPALLSFPVGEWVCTLC 46
DEXQc_SHPRH cd18070
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ...
700-898 2.22e-10

DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously expressed protein that contains motifs characteristic of several DNA repair proteins, transcription factors, and helicases. SHPRH is a functional homolog of S. cerevisiae RAD5 and is involved in DNA repair. SHPRH is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350828 [Multi-domain]  Cd Length: 257  Bit Score: 63.13  E-value: 2.22e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWLRfsWAQGtdtILADEMGLGKTVQTI----------------------VFLYSLYKEGHSK---GPYLV 754
Cdd:cd18070     1 LLPYQRRAVNWML--VPGG---ILADEMGLGKTVEVLalillhprpdndldaadddsdeMVCCPDCLVAETPvssKATLI 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  755 SAPLSTIINWEREFEMWAPDFYVV-TYTGDKESRSVIRE---------------NEFSFE---DNAIRSGKKVFRMKKEV 815
Cdd:cd18070    76 VCPSAILAQWLDEINRHVPSSLKVlTYQGVKKDGALASPapeilaeydivvttyDVLRTElhyAEANRSNRRRRRQKRYE 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  816 QIKfhvlltsyelitidqAILGSIEWACLVVDEAHRLKNNQSK-------FFRVlNSYKIdyklllTGTPLQNNLEELFH 888
Cdd:cd18070   156 APP---------------SPLVLVEWWRVCLDEAQMVESSTSKaaemarrLPRV-NRWCV------SGTPIQRGLDDLFG 213
                         250
                  ....*....|
gi 119591922  889 LLNFLTPERF 898
Cdd:cd18070   214 LLSFLGVEPF 223
CHROMO smart00298
Chromatin organization modifier domain;
592-625 2.38e-10

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 57.61  E-value: 2.38e-10
                            10        20        30
                    ....*....|....*....|....*....|....
gi 119591922    592 MMIHRILNHSFDKKGDVHYLIKWKDLPYDQCTWE 625
Cdd:smart00298    2 YEVEKILDHRWKKKGELEYLVKWKGYSYSEDTWE 35
PHD_BAZ2A_like cd15545
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B ...
345-387 2.75e-10

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B (BAZ2B); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A. Both BAZ2A and BAZ2B contain a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain. BAZ2B also harbors an extra Apolipophorin-III like domain in its N-terminal region.


Pssm-ID: 277020 [Multi-domain]  Cd Length: 46  Bit Score: 57.32  E-value: 2.75e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 119591922  345 YCEVCQQG---GEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15545     1 SCQICRSGdneDQLLLCDGCDRGYHTYCFKPKMTNVPEGDWFCPEC 46
PHD4_NSD1 cd15656
PHD finger 4 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, ...
418-460 3.06e-10

PHD finger 4 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, also termed H3 Lysine-36 and H4 Lysine-20 specific histone-lysine N-methyltransferase, or androgen receptor coactivator 267 kDa protein, or androgen receptor-associated protein of 267 kDa, or H3-K36-HMTase H4-K20-HMTase, or Lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein, is a lysine methyltransferase that preferentially methylates H3 on Lysine36 (H3-K36) and H4 on Lysine20 (H4-K20), which is primarily associated with active transcription. It plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. It can alter transcription by interacting with the protein NSD1-interacting zinc finger protein 1 (NIZP1). It also mitigates caspase-1 activation by listeriolysin o (LLO) in macrophages, and requires functional LLO for the regulation of IL-1beta secretion. Moreover, NSD1 regulates RNA polymerase II (RNAP II) recruitment to bone morphogenetic protein 4 (BMP4). NSD1 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fourth PHD finger.


Pssm-ID: 277126  Cd Length: 40  Bit Score: 56.95  E-value: 3.06e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  418 FCRVCKDGGELLCCDACPSSYHLHCLNPPLPEipnGEWLCPRC 460
Cdd:cd15656     1 WCFVCSEGGSLLCCESCPAAFHRECLNIDMPE---GSWYCNDC 40
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
345-387 3.62e-10

PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV pX-associated protein 8, or Hepatitis B virus X-associated protein alpha (HBxAPalpha), or p325 subunit of RSF chromatin-remodeling complex, is a novel nuclear protein with histone chaperon function. It is a subunit of an ISWI chromatin remodeling complex, remodeling and spacing factor (RSF), and plays a role in mediating ATPase-dependent chromatin remodeling and conferring tumor aggressiveness in common carcinomas. As an ataxia-telangiectasia mutated (ATM)-dependent chromatin remodeler, Rsf-1 facilitates DNA damage checkpoints and homologous recombination repair. It regulates the mitotic spindle checkpoint and chromosome instability through the association with serine/threonine kinase BubR1 (BubR1) and Hepatitis B virus (HBV) X protein (HBx) in the chromatin fraction during mitosis. It also interacts with cyclin E1 and promotes tumor development. Rsf-1 contains a plant homeodomain (PHD) finger.


Pssm-ID: 277018 [Multi-domain]  Cd Length: 46  Bit Score: 56.89  E-value: 3.62e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 119591922  345 YCEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15543     1 PCRKCGLSDHpewILLCDRCDAGYHTACLRPPLMIIPDGNWFCPPC 46
PHD_TIF1gamma cd15624
PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also ...
345-387 7.81e-10

PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also termed tripartite motif-containing 33 (trim33), or ectodermin, or RFG7, or PTC7, is an E3-ubiquitin ligase that functions as a regulator of transforming growth factor beta (TGFbeta) signaling; it inhibits the Smad4-mediated TGFbeta response by interaction with Smad2/3 or ubiquitylation of Smad4. Moreover, TIF1gamma is an important regulator of transcription during hematopoiesis, as well as a key factor of tumorigenesis. Like other TIF1 family members, TIF1gamma also contains an intrinsic transcriptional silencing function. It can control erythroid cell fate by regulating transcription elongation. It can bind to the anaphase-promoting complex/cyclosome (APC/C) and promotes mitosis. TIF1gamma contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.


Pssm-ID: 277094  Cd Length: 46  Bit Score: 55.82  E-value: 7.81e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  345 YCEVCQQGGEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15624     1 WCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFC 43
PHD_PRKCBP1 cd15538
PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed ...
418-460 8.40e-10

PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), or Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor; the RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a plant homeodomain (PHD) finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277013  Cd Length: 41  Bit Score: 55.80  E-value: 8.40e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  418 FCRVCKDGGELLCCDACPSSYHLHCLnpPLPEIPNGEWLCPRC 460
Cdd:cd15538     1 FCWRCHKEGQVLCCSLCPRVYHKKCL--KLTSEPDEDWVCPEC 41
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
346-387 1.01e-09

PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger of KMT2C and the fourth PHD finger of KMT2D.


Pssm-ID: 276988  Cd Length: 47  Bit Score: 55.56  E-value: 1.01e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  346 CEVCQQG---GEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15513     2 CEGCGKAsdeSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 46
ADDz_Dnmt3 cd11725
ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3 (Dnmt3); Dnmt3 is a de ...
334-393 1.21e-09

ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3 (Dnmt3); Dnmt3 is a de novo DNA methyltransferase family that includes two active enzymes Dnmt3a and -3b and one regulatory factor Dnmt3l. The ADDz domain of Dnmt3 is located in the C-terminal region of Dnmt3, which is an active catalytic domain in Dnmt3a and -b, but lacks some residues for enzymatic activity in Dnmt3l. DNA methylation is an important epigenetic mechanism involved in diverse biological processes such as embryonic development, gene expression, and genomic imprinting. The ADDz_Dnmt3 domain is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger. PHD zinc finger domains have been identified in more than 40 proteins that are mainly involved in chromatin mediated transcriptional control; the classical PHD zinc finger has a C4-H-C3 motif that spans about 50-80 amino acids. In ADDz, the conserved histidine residue of the PHD finger is replaced by a cysteine, and an additional zinc finger C2-C2 like motif is located about twenty residues upstream of the C4-C-C3 motif.


Pssm-ID: 277251 [Multi-domain]  Cd Length: 108  Bit Score: 57.40  E-value: 1.21e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 119591922  334 DGDGYetdhQDYCEVCQQGGEIILCDT--CPRAYHLVCLD----PE-LEKAPEG-KWSCPHCEKEGIQ 393
Cdd:cd11725    42 DDDGY----QMYCTICGGGGEVVLCDNpdCTRVYCTECLDlllgPGaVAKILESdPWFCFLCSPESNS 105
PHD4_NSD2 cd15657
PHD finger 4 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed ...
418-460 1.38e-09

PHD finger 4 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed histone-lysine N-methyltransferase NSD2, or multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). NSD2 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, a high mobility group (HMG) box, five PHD (plant-homeodomain) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD fingers mediate chromatin interaction and recognition of histone marks. This model corresponds to the fourth PHD finger.


Pssm-ID: 277127  Cd Length: 41  Bit Score: 55.01  E-value: 1.38e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  418 FCRVCKDGGELLCCDACPSSYHLHCLNpplPEIPNGEWLCPRC 460
Cdd:cd15657     1 WCFVCSKGGSLLCCESCPAAFHPDCLN---IEMPDGSWFCNDC 40
DEXQc_bact_SNF2 cd18013
DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 ...
700-887 1.76e-09

DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The Snf2 family comprise a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. The bacterial SNF2 present in this family are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350771 [Multi-domain]  Cd Length: 218  Bit Score: 60.06  E-value: 1.76e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGLNWLRFSWAQGtdtILADeMGLGKTVQTIVFLYSLYKEGhSKGPYLVSAPLSTIIN-WEREFEMWapdfyvv 778
Cdd:cd18013     1 PHPYQKVAINFIIEHPYCG---LFLD-MGLGKTVTTLTALSDLQLDD-FTRRVLVIAPLRVARStWPDEVEKW------- 68
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  779 tytgdkesrSVIRENEFSFednAIRSGKKvfrMKKEVQIKFHVLLTSYELIT-IDQAILGSIEWACLVVDEAHRLKNNQS 857
Cdd:cd18013    69 ---------NHLRNLTVSV---AVGTERQ---RSKAANTPADLYVINRENLKwLVNKSGDPWPFDMVVIDELSSFKSPRS 133
                         170       180       190
                  ....*....|....*....|....*....|..
gi 119591922  858 KFFRVLNSY--KIDYKLLLTGTPLQNNLEELF 887
Cdd:cd18013   134 KRFKALRKVrpVIKRLIGLTGTPSPNGLMDLW 165
PHD5_NSD2 cd15660
PHD finger 5 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed ...
345-385 1.83e-09

PHD finger 5 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed histone-lysine N-methyltransferase NSD2, or multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). NSD2 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, a high mobility group (HMG) box, five PHD (plant-homeodomain) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD fingers mediate chromatin interaction and recognition of histone marks. This model corresponds to the fifth PHD finger.


Pssm-ID: 277130  Cd Length: 43  Bit Score: 54.94  E-value: 1.83e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  345 YCEVCQQGGEIILCD--TCPRAYHLVCLDpeLEKAPEGKWSCP 385
Cdd:cd15660     1 ECFRCGDGGQLVLCDrkSCTKAYHLSCLG--LTKRPFGKWECP 41
PHD_BAZ2A cd15629
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also ...
346-387 2.05e-09

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. It contains a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277099  Cd Length: 47  Bit Score: 54.86  E-value: 2.05e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  346 CEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15629     2 CLVCRKGDNdeyLLLCDGCDRGCHMYCHRPKMLQVPEGDWFCPNC 46
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
419-460 2.06e-09

PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger of KMT2C and the fourth PHD finger of KMT2D.


Pssm-ID: 276988  Cd Length: 47  Bit Score: 54.79  E-value: 2.06e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  419 CRVC---KDGGELLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15513     2 CEGCgkaSDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 46
PHD1_Snt2p_like cd15497
PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and ...
419-460 2.91e-09

PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins; Snt2p is a yeast protein that may function in multiple stress pathways. It coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress through interaction with Ecm5 and the Rpd3 deacetylase. Snt2p contains a bromo adjacent homology (BAH) domain, two canonical Cys4HisCys3 plant homeodomain (PHD) fingers, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain; this model corresponds to the first canonical Cys4HisCys3 PHD finger.


Pssm-ID: 276972  Cd Length: 48  Bit Score: 54.24  E-value: 2.91e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 119591922  419 CRVCKD---GGELLCCDACPSSYHLHCLNPPLPEIPNGE--WLCPRC 460
Cdd:cd15497     2 CKVCKEwcaSDDSVRCDECKVSYHLLCVDPPLTKKPNRGfvWSCAPC 48
PHD_TIF1beta cd15623
PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also ...
419-460 3.32e-09

PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also termed Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), or KRAB-interacting protein 1 (KRIP-1), or nuclear co-repressor KAP-1, or RING finger protein 96, or tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, acts as a nuclear co-repressor that plays a role in transcription and in DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. In addition, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. TIF1-beta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), which can interact with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and mediates homo- and heterodimerization, a plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region, which interact with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.


Pssm-ID: 277093  Cd Length: 43  Bit Score: 54.04  E-value: 3.32e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 119591922  419 CRVCKDGGELLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15623     2 CRVCQKAGALVMCDQCEFCFHLDCHLPALQEVPGEDWKCLLC 43
PHD2_KMT2D cd15595
PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
419-460 5.79e-09

PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 277070  Cd Length: 46  Bit Score: 53.46  E-value: 5.79e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  419 CRVCKDGGE---LLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15595     2 CQTCRKPGEdskMLVCEACDKGYHTFCLKPAMESLPTDSWKCKAC 46
PHD_UHRF1 cd15616
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); ...
419-460 6.17e-09

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); UHRF1 (also termed inverted CCAAT box-binding protein of 90 kDa, nuclear protein 95, nuclear zinc finger protein Np95 (Np95), RING finger protein 106, transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1) is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET and RING finger associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitylation has an essential role in maintaining DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD finger targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibit both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1.


Pssm-ID: 277088  Cd Length: 47  Bit Score: 53.43  E-value: 6.17e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 119591922  419 CRVC---KDGGELLCCDACPSSYHLHCLNPPLPEIPN-GEWLCPRC 460
Cdd:cd15616     2 CHVCggkQDPDKQLMCDECDMAFHIYCLNPPLSSIPDdEDWYCPEC 47
PHD_BAZ2A cd15629
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also ...
419-460 7.09e-09

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. It contains a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277099  Cd Length: 47  Bit Score: 53.32  E-value: 7.09e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  419 CRVCKDGGE---LLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15629     2 CLVCRKGDNdeyLLLCDGCDRGCHMYCHRPKMLQVPEGDWFCPNC 46
PHD_PHRF1 cd15536
PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also ...
345-387 7.21e-09

PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also termed KIAA1542, or CTD-binding SR-like protein rA9, is a ubiquitin ligase that induces the ubiquitination of TGIF (TG-interacting factor) at lysine 130. It acts as a tumor suppressor that promotes the transforming growth factor (TGF)-beta cytostatic program through selective release of TGIF-driven promyelocytic leukemia protein (PML) inactivation. PHRF1 contains a plant homeodomain (PHD) finger and a RING finger.


Pssm-ID: 277011  Cd Length: 46  Bit Score: 53.19  E-value: 7.21e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 119591922  345 YCEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15536     1 YCEVCGRSDRedrLLLCDGCDAGYHMECLTPPLDEVPIEEWFCPEC 46
PHD5_NSD3 cd15661
PHD finger 5 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed ...
418-458 7.31e-09

PHD finger 5 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed histone-lysine N-methyltransferase NSD3, or protein whistle, or WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, or Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1-like protein 1, or WHSC1L1), is a lysine methyltransferase encoded by gene NSD3, which is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD3 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, five plant-homeodomain (PHD) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fifth PHD finger.


Pssm-ID: 277131  Cd Length: 43  Bit Score: 53.05  E-value: 7.31e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  418 FCRVCKDGGELLCCDA--CPSSYHLHCLNppLPEIPNGEWLCP 458
Cdd:cd15661     1 YCFQCGDGGELVMCDKkdCPKAYHLLCLN--LTQPPYGKWECP 41
PHD1_KDM5C_5D cd15604
PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
346-387 1.01e-08

PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family includes KDM5C and KDM5D, both of which belong to the JARID subfamily within the JmjC proteins. KDM5C (also termed Histone demethylase JARID1C, Jumonji/ARID domain-containing protein 1C, SmcX, or Xe169) is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D (also termed Histocompatibility Y antigen (H-Y), Histone demethylase JARID1D, Jumonji/ARID domain-containing protein 1D, or SmcY) is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 andH3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. Both KDM5C and KDM5D contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277077  Cd Length: 46  Bit Score: 52.92  E-value: 1.01e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  346 CEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15604     2 CRMCSRGDEddkLLLCDGCDDNYHTFCLLPPLPEPPKGIWRCPKC 46
PHD1_KDM5A_like cd15515
PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar ...
346-387 1.02e-08

PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar proteins; The JARID subfamily within the JmjC proteins includes Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog, protein little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me2 and H3K4me3), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. This family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent H3K4me3 demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two or three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 276990  Cd Length: 46  Bit Score: 52.78  E-value: 1.02e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  346 CEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15515     2 CQVCGRGDDedkLLLCDGCDDSYHTFCLIPPLPDIPPGDWRCPKC 46
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
346-387 1.31e-08

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the second PHD finger.


Pssm-ID: 277069  Cd Length: 46  Bit Score: 52.63  E-value: 1.31e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  346 CEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15594     2 CQTCRQPGDdnkMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
346-387 1.50e-08

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277000  Cd Length: 47  Bit Score: 52.37  E-value: 1.50e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 119591922  346 CEVCqqGGE-----IILCDTCPRAYHLVCLDPELEKAP-EGKWSCPHC 387
Cdd:cd15525     2 CHVC--GGKqdpekQLLCDECDMAYHLYCLDPPLTSLPdDDEWYCPDC 47
PHD2_KMT2D cd15595
PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
346-387 1.63e-08

PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 277070  Cd Length: 46  Bit Score: 52.31  E-value: 1.63e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  346 CEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15595     2 CQTCRKPGEdskMLVCEACDKGYHTFCLKPAMESLPTDSWKCKAC 46
PHD_TIF1beta cd15623
PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also ...
346-387 1.72e-08

PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also termed Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), or KRAB-interacting protein 1 (KRIP-1), or nuclear co-repressor KAP-1, or RING finger protein 96, or tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, acts as a nuclear co-repressor that plays a role in transcription and in DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. In addition, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. TIF1-beta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), which can interact with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and mediates homo- and heterodimerization, a plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region, which interact with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.


Pssm-ID: 277093  Cd Length: 43  Bit Score: 52.11  E-value: 1.72e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 119591922  346 CEVCQQGGEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15623     2 CRVCQKAGALVMCDQCEFCFHLDCHLPALQEVPGEDWKCLLC 43
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
346-387 1.72e-08

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2 (also termed Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2) was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs,p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277089  Cd Length: 47  Bit Score: 52.26  E-value: 1.72e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 119591922  346 CEVC---QQGGEIILCDTCPRAYHLVCLDPELEKAPEGK-WSCPHC 387
Cdd:cd15617     2 CYVCggkQDAHMQLLCDECNMAYHIYCLNPPLDKIPEDEdWYCPSC 47
PHD1_Snt2p_like cd15497
PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and ...
345-387 1.83e-08

PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins; Snt2p is a yeast protein that may function in multiple stress pathways. It coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress through interaction with Ecm5 and the Rpd3 deacetylase. Snt2p contains a bromo adjacent homology (BAH) domain, two canonical Cys4HisCys3 plant homeodomain (PHD) fingers, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain; this model corresponds to the first canonical Cys4HisCys3 PHD finger.


Pssm-ID: 276972  Cd Length: 48  Bit Score: 51.93  E-value: 1.83e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 119591922  345 YCEVCQQ---GGEIILCDTCPRAYHLVCLDPELEKAPEGK--WSCPHC 387
Cdd:cd15497     1 SCKVCKEwcaSDDSVRCDECKVSYHLLCVDPPLTKKPNRGfvWSCAPC 48
PHD1_MTF2_PHF19_like cd15499
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
346-389 2.54e-08

PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) family proteins MTF2, PHF19, and similar proteins; The family includes two PCL family proteins, metal-response element-binding transcription factor 2 (MTF2/PCL2) and PHF19/PCL3, which are homologs of PHD finger protein1 (PHF1). PCL family proteins are accessory components of the polycomb repressive complex 2 (PRC2) core complex and all contain an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. They specifically recognize tri-methylated H3K36 (H3K36me3) through their N-terminal Tudor domains. The interaction between their Tudor domains and H3K36me3 is critical for both the targeting and spreading of PRC2 into active chromatin regions and for the maintenance of optimal repression of poised developmental genes where PCL proteins, H3K36me3, and H3K27me3 coexist. Moreover, unlike other PHD finger-containing proteins, the first PHD fingers of PCL proteins do not display histone H3K4 binding affinity and they do not affect the Tudor domain binding to histones. This model corresponds to the first PHD finger.


Pssm-ID: 276974  Cd Length: 53  Bit Score: 51.73  E-value: 2.54e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 119591922  346 CEVCQ-----QGGEIILCDTCPRAYHLVCLDPELEKAP---EGKWSCPHCEK 389
Cdd:cd15499     2 CSICGgaearDGNEILICDKCDKGYHQLCHSPKVRTSPlegDEKWFCSRCVF 53
PHD2_PHF12_Rco1 cd15534
PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, ...
418-459 2.74e-08

PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, also termed PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. PHF12 contains two plant homeodomain (PHD) zinc fingers followed by a polybasic region. The PHD fingers function downstream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides. This subfamily also includes yeast transcriptional regulatory protein Rco1 and similar proteins. Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two PHD fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the second PHD finger.


Pssm-ID: 277009  Cd Length: 47  Bit Score: 51.58  E-value: 2.74e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 119591922  418 FCRVCKDGGE---LLCCDACPSSYHLHCLNPPLPEIPN-GEWLCPR 459
Cdd:cd15534     1 VCFKCNRSCRvapLIQCDYCPLLFHLDCLDPPLTHPPAtGRWMCPN 46
PHD2_d4 cd15530
PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three ...
345-387 2.76e-08

PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes by changing the condensed/decondensed state of chromatin in the nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro-specific gene clusters. The d4 family proteins show distinct domain organization with domain 2/3 in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc finger in the central part and two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This model corresponds to the second PHD finger.


Pssm-ID: 277005  Cd Length: 46  Bit Score: 51.62  E-value: 2.76e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 119591922  345 YCEVC---QQGGEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15530     1 SCSLCgtsENDDQLLFCDDCDRGYHMYCLSPPMSEPPEGSWSCHLC 46
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
419-460 3.09e-08

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 276985  Cd Length: 46  Bit Score: 51.28  E-value: 3.09e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  419 CRVCKDGGE---LLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15510     2 CQACRQPGDdtkMLVCETCDKGYHTSCLRPVMSSIPKYGWKCKNC 46
PHD_SP110_140 cd15626
PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family ...
346-387 3.21e-08

PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family includes nuclear body proteins SP100, SP140, and similar proteins. Sp110, also termed interferon-induced protein 41/75, or speckled 110 kDa, or transcriptional coactivator Sp110, is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. Sp110 gene polymorphisms may be associated with susceptibility to tuberculosis in Chinese population. Sp110 contains a Sp100-like domain, a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD). SP140, also termed lymphoid-restricted homolog of Sp100 (LYSp100), or nuclear autoantigen Sp-140, or speckled 140 kDa, is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus's viral infectivity factor (Vif) protein. Sp140 contains a nuclear localization signal, a dimerization domain (HSR or CARD domain), a SAND domain, a PHD finger, and a BRD.


Pssm-ID: 277096  Cd Length: 42  Bit Score: 51.27  E-value: 3.21e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 119591922  346 CEVCQQGGEIILCDTCPRAYHLVCLDPELEkAPEGKWSCPHC 387
Cdd:cd15626     2 CEVCGQEGKLFCCCTCSRVFHEDCHIPPVE-AQRSPWSCTFC 42
PHD4_NSD3 cd15658
PHD finger 4 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed ...
345-387 3.59e-08

PHD finger 4 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed histone-lysine N-methyltransferase NSD3, or protein whistle, or WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, or Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1-like protein 1, or WHSC1L1), is a lysine methyltransferase encoded by gene NSD3, which is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD3 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, five plant-homeodomain (PHD) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fourth PHD finger.


Pssm-ID: 277128  Cd Length: 40  Bit Score: 51.07  E-value: 3.59e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  345 YCEVCQQGGEIILCDTCPRAYHLVCLDPELekaPEGKWSCPHC 387
Cdd:cd15658     1 FCFVCARGGRLLCCESCPASFHPECLSIEM---PEGCWNCNEC 40
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
346-387 3.87e-08

PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis antigen 31 (CT31), Histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A)) is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of pregnant females and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277076  Cd Length: 46  Bit Score: 51.11  E-value: 3.87e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  346 CEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15603     2 CLVCGSGNDedrLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 46
PHD1_Lid_like cd15605
PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar ...
346-387 4.22e-08

PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar proteins; Drosophila melanogaster Lid, also termed Retinoblastoma-binding protein 2 homolog, is identified genetically as a trithorax group (trxG) protein that is a Drosophila homolog of the human protein JARID1A/kdm5A, a member of the JARID subfamily within the JmjC proteins. Lid functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Lid contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger of Lid.


Pssm-ID: 277078  Cd Length: 46  Bit Score: 50.91  E-value: 4.22e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  346 CEVCQQG-GE--IILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15605     2 CHTCGRGdGEesMLLCDGCDDSYHTFCLLPPLSEVPKGDWRCPKC 46
PHD_SP110_140 cd15626
PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family ...
419-460 4.89e-08

PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family includes nuclear body proteins SP100, SP140, and similar proteins. Sp110, also termed interferon-induced protein 41/75, or speckled 110 kDa, or transcriptional coactivator Sp110, is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. Sp110 gene polymorphisms may be associated with susceptibility to tuberculosis in Chinese population. Sp110 contains a Sp100-like domain, a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD). SP140, also termed lymphoid-restricted homolog of Sp100 (LYSp100), or nuclear autoantigen Sp-140, or speckled 140 kDa, is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus's viral infectivity factor (Vif) protein. Sp140 contains a nuclear localization signal, a dimerization domain (HSR or CARD domain), a SAND domain, a PHD finger, and a BRD.


Pssm-ID: 277096  Cd Length: 42  Bit Score: 50.89  E-value: 4.89e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 119591922  419 CRVCKDGGELLCCDACPSSYHLHCLNPPLpEIPNGEWLCPRC 460
Cdd:cd15626     2 CEVCGQEGKLFCCCTCSRVFHEDCHIPPV-EAQRSPWSCTFC 42
PHD3_PHF14 cd15563
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
346-387 5.11e-08

PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the third PHD finger.


Pssm-ID: 277038  Cd Length: 49  Bit Score: 50.86  E-value: 5.11e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 119591922  346 CEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGK---WSCPHC 387
Cdd:cd15563     2 CCVCKQTGDnsqLVRCDECKLCYHFGCLDPPLKKSPKQRgygWVCEEC 49
PHD_PRHA_like cd15504
PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and ...
345-387 5.83e-08

PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and similar proteins; PRHA is a homeodomain protein encoded by a single-copy Arabidopsis thaliana homeobox gene, prha. It shows the capacity to bind to TAATTG core sequence elements but requires additional adjacent bases for high-affinity binding. PRHA contains a plant homeodomain (PHD) finger, a homeodomain, peptide repeats and a putative leucine zipper dimerization domain.


Pssm-ID: 276979  Cd Length: 53  Bit Score: 50.90  E-value: 5.83e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 119591922  345 YCEVCQQGGE-----IILCD-TCPRAYHLVCLDPELEK----APEGKWSCPHC 387
Cdd:cd15504     1 FCAKCQSGEAspdndILLCDgGCNRAYHQKCLEPPLLTedipPEDEGWLCPLC 53
PHD1_KDM5A cd15602
PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
346-390 6.12e-08

PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2)) was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as a trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277075  Cd Length: 49  Bit Score: 50.72  E-value: 6.12e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 119591922  346 CEVCQQGG---EIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHCEKE 390
Cdd:cd15602     2 CLFCGRGNnedKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCVAE 49
CD2_tandem_CHD5-9_like cd18663
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, ...
589-630 1.03e-07

repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD5, CHD6, CHD7, CHD8, and CHD9. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. CHD6, CHD7, and CHD8 enzymes have been demonstrated to have different substrate specificities and remodeling activities. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349310 [Multi-domain]  Cd Length: 59  Bit Score: 50.37  E-value: 1.03e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 119591922  589 PEWMMIHRILNHSFDKKGD-----VHYLIKWKDLPYDQCTWEI-DDID 630
Cdd:cd18663     1 PDYVEVDRILDVSVSTDPNtgepvTHYLVKWCSLPYEDSTWELeEDVD 48
PHD4_NSD1 cd15656
PHD finger 4 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, ...
345-387 1.09e-07

PHD finger 4 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, also termed H3 Lysine-36 and H4 Lysine-20 specific histone-lysine N-methyltransferase, or androgen receptor coactivator 267 kDa protein, or androgen receptor-associated protein of 267 kDa, or H3-K36-HMTase H4-K20-HMTase, or Lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein, is a lysine methyltransferase that preferentially methylates H3 on Lysine36 (H3-K36) and H4 on Lysine20 (H4-K20), which is primarily associated with active transcription. It plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. It can alter transcription by interacting with the protein NSD1-interacting zinc finger protein 1 (NIZP1). It also mitigates caspase-1 activation by listeriolysin o (LLO) in macrophages, and requires functional LLO for the regulation of IL-1beta secretion. Moreover, NSD1 regulates RNA polymerase II (RNAP II) recruitment to bone morphogenetic protein 4 (BMP4). NSD1 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fourth PHD finger.


Pssm-ID: 277126  Cd Length: 40  Bit Score: 49.63  E-value: 1.09e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  345 YCEVCQQGGEIILCDTCPRAYHLVCLDPELekaPEGKWSCPHC 387
Cdd:cd15656     1 WCFVCSEGGSLLCCESCPAAFHRECLNIDM---PEGSWYCNDC 40
PHD2_d4 cd15530
PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three ...
419-460 1.35e-07

PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes by changing the condensed/decondensed state of chromatin in the nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro-specific gene clusters. The d4 family proteins show distinct domain organization with domain 2/3 in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc finger in the central part and two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This model corresponds to the second PHD finger.


Pssm-ID: 277005  Cd Length: 46  Bit Score: 49.69  E-value: 1.35e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  419 CRVC---KDGGELLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15530     2 CSLCgtsENDDQLLFCDDCDRGYHMYCLSPPMSEPPEGSWSCHLC 46
PHD3_NSD cd15566
PHD finger 3 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
418-459 1.59e-07

PHD finger 3 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the third PHD finger.


Pssm-ID: 277041  Cd Length: 48  Bit Score: 49.35  E-value: 1.59e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 119591922  418 FCRVC-----KDGGELLCCDACPSSYHLHCLNPPLPEIPNGEWLCPR 459
Cdd:cd15566     1 TCATCeasgdGSSGKLVRCIRCPRAYHAGCIPAGSKLLNKKLIICPK 47
PHD2_PHF14 cd15562
PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
346-387 1.80e-07

PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the second PHD finger.


Pssm-ID: 277037  Cd Length: 50  Bit Score: 49.33  E-value: 1.80e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 119591922  346 CEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGK----WSCPHC 387
Cdd:cd15562     2 CGICKKSNDqhlLALCDTCKLYYHLGCLDPPLTRMPKKTknsgWQCSEC 50
CHROMO smart00298
Chromatin organization modifier domain;
466-546 3.33e-07

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 48.75  E-value: 3.33e-07
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922    466 KGKVQRILHWRWTEppapfmvglpgpdvepslpppkplEGipEREFFVKWAGLSYWHCSWVKELQLELYHTVMYRNYQRK 545
Cdd:smart00298    1 EYEVEKILDHRWKK------------------------KG--ELEYLVKWKGYSYSEDTWEPEENLLNCSKKLDNYKKKE 54

                    .
gi 119591922    546 N 546
Cdd:smart00298   55 R 55
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
346-387 3.54e-07

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 276985  Cd Length: 46  Bit Score: 48.58  E-value: 3.54e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  346 CEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15510     2 CQACRQPGDdtkMLVCETCDKGYHTSCLRPVMSSIPKYGWKCKNC 46
PHD_BAZ2B cd15630
PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also ...
418-460 3.76e-07

PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A, which is the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP-and histone H4 tail-dependent fashion. BAZ2B contains a TAM (TIP5/ARBP/MBD) domain, an Apolipophorin-III like domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277100  Cd Length: 49  Bit Score: 48.43  E-value: 3.76e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 119591922  418 FCRVCKDGGE---LLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15630     2 YCQICRKGDNeelLLLCDGCDKGCHTYCHRPKITTIPEGDWFCPAC 47
PHD_PRHA_like cd15504
PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and ...
418-460 4.10e-07

PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and similar proteins; PRHA is a homeodomain protein encoded by a single-copy Arabidopsis thaliana homeobox gene, prha. It shows the capacity to bind to TAATTG core sequence elements but requires additional adjacent bases for high-affinity binding. PRHA contains a plant homeodomain (PHD) finger, a homeodomain, peptide repeats and a putative leucine zipper dimerization domain.


Pssm-ID: 276979  Cd Length: 53  Bit Score: 48.59  E-value: 4.10e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 119591922  418 FCRVCKDGGE------LLCCDACPSSYHLHCLNPPL--PEIPNGE--WLCPRC 460
Cdd:cd15504     1 FCAKCQSGEAspdndiLLCDGGCNRAYHQKCLEPPLltEDIPPEDegWLCPLC 53
PRK04914 PRK04914
RNA polymerase-associated protein RapA;
840-947 4.19e-07

RNA polymerase-associated protein RapA;


Pssm-ID: 235319 [Multi-domain]  Cd Length: 956  Bit Score: 55.23  E-value: 4.19e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  840 EWACLVVDEAHRL---KNNQSKFFRVLN--SYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEE---FADI 911
Cdd:PRK04914  272 EWDLLVVDEAHHLvwsEEAPSREYQVVEqlAEVIPGVLLLTATPEQLGQESHFARLRLLDPDRFHDYEAFVEEqqqYRPV 351
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 119591922  912 SK------------EDQIKKLHDLLGPH----MLRRLKADVFKNMPAKTELI 947
Cdd:PRK04914  352 ADavqallageklsDDALNALGELLGEQdiepLLQAANSDSEEAQAARQELI 403
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
419-460 4.81e-07

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the second PHD finger.


Pssm-ID: 277069  Cd Length: 46  Bit Score: 48.01  E-value: 4.81e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  419 CRVCKDGGE---LLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15594     2 CQTCRQPGDdnkMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
PHD_Phf1p_Phf2p_like cd15502
PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...
418-460 5.10e-07

PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 (Phf1p) and Phf2 (Phf2p); Phf1p and Phf2p are components of the SWM histone demethylase complex that specifically demethylates histone H3 at lysine 9 (H3K9me2), a specific tag for epigenetic transcriptional activation. They function as corepressors and play roles in regulating heterochromatin propagation and euchromatic transcription. Both Phf1p and Phf2p contain a plant homeodomain (PHD) finger.


Pssm-ID: 276977  Cd Length: 52  Bit Score: 48.20  E-value: 5.10e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 119591922  418 FCRVCKDG-----GELLCCDACPSSYHLHCLNPP----LPEIPNGEWLCPRC 460
Cdd:cd15502     1 VCIVCQRGhspksNRIVFCDGCNTPYHQLCHDPSiddeVVEDPDAEWFCKKC 52
PHD_BAZ2B cd15630
PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also ...
345-387 5.10e-07

PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A, which is the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP-and histone H4 tail-dependent fashion. BAZ2B contains a TAM (TIP5/ARBP/MBD) domain, an Apolipophorin-III like domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277100  Cd Length: 49  Bit Score: 48.05  E-value: 5.10e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 119591922  345 YCEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15630     2 YCQICRKGDNeelLLLCDGCDKGCHTYCHRPKITTIPEGDWFCPAC 47
ADDz_ATRX cd11726
ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked); ADDz_ATRX is a ...
334-389 6.67e-07

ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked); ADDz_ATRX is a PHD-like zinc finger domain of ATRX, which belongs to the SNF2 family of chromatin remodeling proteins. ATRX is a large chromatin-associated nuclear protein with two domains, ADDz_ATRX at the N-terminus, followed by a C-terminal ATPase/helicase domain. The ADDz_ATRX domain recognizes a specific methylated histone, and this interaction is required for heterochromatin localization of the ATRX protein. Missense mutations in either of the two ATRX domains lead to the X-linked alpha-thalassemia and mental retardation syndrome; however the mutations in the ADDz_ATRX domain produce a more severe disease phenotype that may also relate to disturbing unknown functions or interaction sites of this domain. The ADDz domain is also present in chromatin-associated proteins cytosine-5-methyltransferase 3 (Dnmt3); it is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger. PHD zinc finger domains have been identified in more than 40 proteins that are mainly involved in chromatin mediated transcriptional control; the classical PHD zinc finger has a C4-H-C3 motif that spans about 50-80 amino acids. In ADDz, the conserved histidine residue of the PHD finger is replaced by a cysteine, and an additional zinc finger C2-C2 like motif is located about twenty residues upstream of the C4-C-C3 motif.


Pssm-ID: 277252 [Multi-domain]  Cd Length: 102  Bit Score: 49.23  E-value: 6.67e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 119591922  334 DGDGYETdhqdYCEVCQQGGEIILCDTCPRAYHLVCL-----DPELEKAPE-GKWSCPHCEK 389
Cdd:cd11726    45 DEDGSDE----YCRWCGQGGDLICCDFCPNVFCKKCIkrnlgRAELSRIEEsDKWKCFVCDP 102
PHD_UHRF1 cd15616
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); ...
346-387 7.65e-07

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); UHRF1 (also termed inverted CCAAT box-binding protein of 90 kDa, nuclear protein 95, nuclear zinc finger protein Np95 (Np95), RING finger protein 106, transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1) is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET and RING finger associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitylation has an essential role in maintaining DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD finger targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibit both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1.


Pssm-ID: 277088  Cd Length: 47  Bit Score: 47.65  E-value: 7.65e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 119591922  346 CEVC---QQGGEIILCDTCPRAYHLVCLDPELEKAP-EGKWSCPHC 387
Cdd:cd15616     2 CHVCggkQDPDKQLMCDECDMAFHIYCLNPPLSSIPdDEDWYCPEC 47
PHD2_PHF10 cd15529
PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
419-460 7.70e-07

PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.


Pssm-ID: 277004  Cd Length: 44  Bit Score: 47.30  E-value: 7.70e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  419 CRVC---KDGGELLCCDACPSSYHLHCLNppLPEIPNGEWLCPRC 460
Cdd:cd15529     2 CTKCgdpHDEDKMMFCDQCDRGYHTFCVG--LRSIPDGRWICPLC 44
PHD4_NSD2 cd15657
PHD finger 4 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed ...
345-387 1.24e-06

PHD finger 4 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed histone-lysine N-methyltransferase NSD2, or multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). NSD2 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, a high mobility group (HMG) box, five PHD (plant-homeodomain) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD fingers mediate chromatin interaction and recognition of histone marks. This model corresponds to the fourth PHD finger.


Pssm-ID: 277127  Cd Length: 41  Bit Score: 46.92  E-value: 1.24e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  345 YCEVCQQGGEIILCDTCPRAYHLVCLDPELekaPEGKWSCPHC 387
Cdd:cd15657     1 WCFVCSKGGSLLCCESCPAAFHPDCLNIEM---PDGSWFCNDC 40
TNG2 COG5034
Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];
334-390 1.72e-06

Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];


Pssm-ID: 227367 [Multi-domain]  Cd Length: 271  Bit Score: 51.86  E-value: 1.72e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 119591922  334 DGDGYETDHQDYCeVCQQG--GEIILCDT--CPRA-YHLVCLDpeLEKAPEGKWSCPHCEKE 390
Cdd:COG5034   212 SSEDNSEGEELYC-FCQQVsyGQMVACDNanCKREwFHLECVG--LKEPPKGKWYCPECKKA 270
PHD2_PHF14 cd15562
PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
418-460 1.77e-06

PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the second PHD finger.


Pssm-ID: 277037  Cd Length: 50  Bit Score: 46.63  E-value: 1.77e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 119591922  418 FCRVCK---DGGELLCCDACPSSYHLHCLNPPLPEIP----NGEWLCPRC 460
Cdd:cd15562     1 SCGICKksnDQHLLALCDTCKLYYHLGCLDPPLTRMPkktkNSGWQCSEC 50
PHD5_NSD1 cd15659
PHD finger 5 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, ...
346-385 1.85e-06

PHD finger 5 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, also termed H3 Lysine-36 and H4 Lysine-20 specific histone-lysine N-methyltransferase, or androgen receptor coactivator 267 kDa protein, or androgen receptor-associated protein of 267 kDa, or H3-K36-HMTase H4-K20-HMTase, or Lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein, is a lysine methyltransferase that preferentially methylates H3 on Lysine36 (H3-K36) and H4 on Lysine20 (H4-K20), which is primarily associated with active transcription. It plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma and glioblastoma formation. It can alter transcription by interacting with the protein NSD1-interacting zinc finger protein 1 (NIZP1). It also mitigates caspase-1 activation by listeriolysin o (LLO) in macrophages, and requires functional LLO for the regulation of IL-1beta secretion. Moreover, NSD1 regulates RNA polymerase II (RNAP II) recruitment to bone morphogenetic protein 4 (BMP4). NSD1 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fifth PHD finger.


Pssm-ID: 277129  Cd Length: 43  Bit Score: 46.47  E-value: 1.85e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 119591922  346 CEVCQQGGEIILCDT--CPRAYHLVCLDpeLEKAPEGKWSCP 385
Cdd:cd15659     2 CFSCGDGGQLVSCKKpgCPKVYHADCLN--LTKRPAGKWECP 41
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
346-387 1.91e-06

PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the first PHD finger.


Pssm-ID: 276984  Cd Length: 48  Bit Score: 46.53  E-value: 1.91e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 119591922  346 CEVCQQGGEI---ILCDTCPRAYHLVCLDPELEKAPEGK--WSCPHC 387
Cdd:cd15509     2 CAVCDSPGDLsdlLFCTSCGQHYHGSCLDPAVRPTPLVRagWQCPEC 48
PHD2_PHF10 cd15529
PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
346-387 2.03e-06

PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.


Pssm-ID: 277004  Cd Length: 44  Bit Score: 46.15  E-value: 2.03e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  346 CEVCQQGG---EIILCDTCPRAYHLVCLDpeLEKAPEGKWSCPHC 387
Cdd:cd15529     2 CTKCGDPHdedKMMFCDQCDRGYHTFCVG--LRSIPDGRWICPLC 44
PHD5_NSD2 cd15660
PHD finger 5 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed ...
419-458 2.86e-06

PHD finger 5 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed histone-lysine N-methyltransferase NSD2, or multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). NSD2 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, a high mobility group (HMG) box, five PHD (plant-homeodomain) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD fingers mediate chromatin interaction and recognition of histone marks. This model corresponds to the fifth PHD finger.


Pssm-ID: 277130  Cd Length: 43  Bit Score: 45.70  E-value: 2.86e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 119591922  419 CRVCKDGGELLCCD--ACPSSYHLHCLNppLPEIPNGEWLCP 458
Cdd:cd15660     2 CFRCGDGGQLVLCDrkSCTKAYHLSCLG--LTKRPFGKWECP 41
PHD_Phf1p_Phf2p_like cd15502
PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...
346-387 3.01e-06

PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 (Phf1p) and Phf2 (Phf2p); Phf1p and Phf2p are components of the SWM histone demethylase complex that specifically demethylates histone H3 at lysine 9 (H3K9me2), a specific tag for epigenetic transcriptional activation. They function as corepressors and play roles in regulating heterochromatin propagation and euchromatic transcription. Both Phf1p and Phf2p contain a plant homeodomain (PHD) finger.


Pssm-ID: 276977  Cd Length: 52  Bit Score: 45.89  E-value: 3.01e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 119591922  346 CEVCQQG-----GEIILCDTCPRAYHLVCLDPELEKA----PEGKWSCPHC 387
Cdd:cd15502     2 CIVCQRGhspksNRIVFCDGCNTPYHQLCHDPSIDDEvvedPDAEWFCKKC 52
PHD1_NSD1_2 cd15648
PHD finger 1 found in nuclear receptor-binding SET domain-containing protein NSD1 and NSD2; ...
346-387 3.32e-06

PHD finger 1 found in nuclear receptor-binding SET domain-containing protein NSD1 and NSD2; NSD1, also termed H3 Lysine-36 and H4 Lysine-20 specific histone-lysine N-methyltransferase, or androgen receptor coactivator 267 kDa protein, or androgen receptor-associated protein of 267 kDa, or H3-K36-HMTase H4-K20-HMTase, or Lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein, is a lysine methyltransferase that preferentially methylates H3 on Lysine36 (H3-K36) and H4 on Lysine20 (H4-K20), which is primarily associated with active transcription. It plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. It can alter transcription by interacting with the protein NSD1-interacting zinc finger protein 1 (NIZP1). It also mitigates caspase-1 activation by listeriolysin o (LLO) in macrophages, and requires functional LLO for the regulation of IL-1beta secretion. Moreover, NSD1 regulates RNA polymerase II (RNAP II) recruitment to bone morphogenetic protein 4 (BMP4). NSD2, also termed histone-lysine N-methyltransferase NSD2, or multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). Both NSD1 and NSD2 contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). In addition, NSD2 harbors a high mobility group (HMG) box. The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD fingers mediate chromatin interaction and recognition of histone marks. This model corresponds to the first PHD finger.


Pssm-ID: 277118  Cd Length: 43  Bit Score: 45.54  E-value: 3.32e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  346 CEVCQQGGEIILCD-TCPRAYHLVCLDpeLEKAPEGKWSCPHC 387
Cdd:cd15648     2 CQVCEKPGELLLCEgQCCGAFHLDCIG--LSEMPSGKFICDEC 42
PHD2_PHF12_Rco1 cd15534
PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, ...
346-385 3.37e-06

PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, also termed PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. PHF12 contains two plant homeodomain (PHD) zinc fingers followed by a polybasic region. The PHD fingers function downstream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides. This subfamily also includes yeast transcriptional regulatory protein Rco1 and similar proteins. Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two PHD fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the second PHD finger.


Pssm-ID: 277009  Cd Length: 47  Bit Score: 45.80  E-value: 3.37e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 119591922  346 CEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPE-GKWSCP 385
Cdd:cd15534     2 CFKCNRSCRvapLIQCDYCPLLFHLDCLDPPLTHPPAtGRWMCP 45
PHD5_NSD1 cd15659
PHD finger 5 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, ...
419-458 3.53e-06

PHD finger 5 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, also termed H3 Lysine-36 and H4 Lysine-20 specific histone-lysine N-methyltransferase, or androgen receptor coactivator 267 kDa protein, or androgen receptor-associated protein of 267 kDa, or H3-K36-HMTase H4-K20-HMTase, or Lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein, is a lysine methyltransferase that preferentially methylates H3 on Lysine36 (H3-K36) and H4 on Lysine20 (H4-K20), which is primarily associated with active transcription. It plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma and glioblastoma formation. It can alter transcription by interacting with the protein NSD1-interacting zinc finger protein 1 (NIZP1). It also mitigates caspase-1 activation by listeriolysin o (LLO) in macrophages, and requires functional LLO for the regulation of IL-1beta secretion. Moreover, NSD1 regulates RNA polymerase II (RNAP II) recruitment to bone morphogenetic protein 4 (BMP4). NSD1 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fifth PHD finger.


Pssm-ID: 277129  Cd Length: 43  Bit Score: 45.70  E-value: 3.53e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 119591922  419 CRVCKDGGELLCCD--ACPSSYHLHCLNppLPEIPNGEWLCP 458
Cdd:cd15659     2 CFSCGDGGQLVSCKkpGCPKVYHADCLN--LTKRPAGKWECP 41
PHD_BS69 cd15537
PHD finger found in protein BS69; Protein BS69, also termed zinc finger MYND domain-containing ...
418-460 4.20e-06

PHD finger found in protein BS69; Protein BS69, also termed zinc finger MYND domain-containing protein 11 (ZMYND11 or ZMY11), is a ubiquitously expressed nuclear protein acting as a transcriptional co-repressor in association with various transcription factors. It was originally identified as an adenovirus 5 E1A-binding protein that inhibits E1A transactivation, as well as c-Myb transcription. It also mediates repression, at least in part, through interaction with the co-repressor N-CoR. Moreover, it interacts with Toll-interleukin 1 receptor domain (TIR)-containing adaptor molecule-1 (TICAM-1, also named TRIF) to facilitate NF-kappaB activation and type I IFN induction. It associates with PIAS1, a SUMO E3 enzyme, and Ubc9, a SUMO E2 enzyme, and plays an inhibitory role in muscle and neuronal differentiation. Moreover, BS69 regulates Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1)/C-terminal activation region 2 (CTAR2)-mediated NF-kappaB activation by interfering with the complex formation between TNFR-associated death domain protein (TRADD) and LMP1/CTAR2. It also cooperates with tumor necrosis factor receptor (TNFR)-associated factor 3 (TRAF3) in the regulation of EBV-derived LMP1/CTAR1-induced NF-kappaB activation. Furthermore, BS69 is involved in the p53-p21Cip1-mediated senescence pathway. BS69 contains a plant homeodomain (PHD) finger, a bromodomain, a proline-tryptophan-tryptophan-proline (PWWP) domain, and a Myeloid translocation protein 8, Nervy and DEAF-1 (MYND) domain.


Pssm-ID: 277012  Cd Length: 43  Bit Score: 45.41  E-value: 4.20e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 119591922  418 FCRVCKDGGELLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15537     1 YCFECHAPGEVLPCSGCFRVYHSDCLSEDFRPDSTSHWTCPVC 43
PHD1_MTF2 cd15578
PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also ...
346-388 5.19e-06

PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also termed metal regulatory transcription factor 2, or metal-response element DNA-binding protein M96, or polycomb-like protein 2 (PCL2), complexes with the polycomb repressive complex-2 (PRC2) in embryonic stem cells and regulates the transcriptional networks during embryonic stem cell self-renewal and differentiation. It recruits the PRC2 complex to the inactive X chromosome and target loci in embryonic stem cells. Moreover, MTF2 is required for PRC2-mediated Hox cluster repression. It activates the Cdkn2a gene and promotes cellular senescence, thus suppressing the catalytic activity of PRC2 locally. MTF2 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. This model corresponds to the first PHD finger.


Pssm-ID: 277053  Cd Length: 53  Bit Score: 45.46  E-value: 5.19e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 119591922  346 CEVCQQG-----GEIILCDTCPRAYHLVCLDPELEK---APEGKWSCPHCE 388
Cdd:cd15578     2 CTVCQDGssespNEIVLCDKCGQGYHQLCHNPKIDSsvlDPDVPWLCRQCV 52
PHD1_MTF2_PHF19_like cd15499
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
419-462 5.38e-06

PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) family proteins MTF2, PHF19, and similar proteins; The family includes two PCL family proteins, metal-response element-binding transcription factor 2 (MTF2/PCL2) and PHF19/PCL3, which are homologs of PHD finger protein1 (PHF1). PCL family proteins are accessory components of the polycomb repressive complex 2 (PRC2) core complex and all contain an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. They specifically recognize tri-methylated H3K36 (H3K36me3) through their N-terminal Tudor domains. The interaction between their Tudor domains and H3K36me3 is critical for both the targeting and spreading of PRC2 into active chromatin regions and for the maintenance of optimal repression of poised developmental genes where PCL proteins, H3K36me3, and H3K27me3 coexist. Moreover, unlike other PHD finger-containing proteins, the first PHD fingers of PCL proteins do not display histone H3K4 binding affinity and they do not affect the Tudor domain binding to histones. This model corresponds to the first PHD finger.


Pssm-ID: 276974  Cd Length: 53  Bit Score: 45.18  E-value: 5.38e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 119591922  419 CRVCK-----DGGELLCCDACPSSYHLHCLNPPL---PEIPNGEWLCPRCTC 462
Cdd:cd15499     2 CSICGgaearDGNEILICDKCDKGYHQLCHSPKVrtsPLEGDEKWFCSRCVF 53
ResIII pfam04851
Type III restriction enzyme, res subunit;
699-878 7.04e-06

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 48.05  E-value: 7.04e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922   699 TLHPYQLEGLNWLRFSWAQGTDTILAdEM--GLGKTVQTIVFLYSLYKEGHSKgPYLVSAPLSTIIN-WEREFEMWAPDf 775
Cdd:pfam04851    3 ELRPYQIEAIENLLESIKNGQKRGLI-VMatGSGKTLTAAKLIARLFKKGPIK-KVLFLVPRKDLLEqALEEFKKFLPN- 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922   776 yvvtytgdkesrsvirenefSFEDNAIRSGKKVFRMKKEVQIKFhvlltsyelITIdQAILGSIEWA----------CLV 845
Cdd:pfam04851   80 --------------------YVEIGEIISGDKKDESVDDNKIVV---------TTI-QSLYKALELAslellpdffdVII 129
                          170       180       190
                   ....*....|....*....|....*....|....
gi 119591922   846 VDEAHRLknnQSKFFR-VLNSYKIDYKLLLTGTP 878
Cdd:pfam04851  130 IDEAHRS---GASSYRnILEYFKPAFLLGLTATP 160
PHD_BRPF cd15572
PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF ...
418-466 8.07e-06

PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF proteins includes BRPF1, BRD1/BRPF2, and BRPF3. They are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277047 [Multi-domain]  Cd Length: 54  Bit Score: 44.91  E-value: 8.07e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 119591922  418 FCRVCKDG-----GELLCCDACPSSYHLHCLNppLPEIPNGEWLCPRCTCPPLK 466
Cdd:cd15572     3 VCCICLDGecqnsNVILFCDMCNLAVHQECYG--VPYIPEGQWLCRRCLQSPSR 54
PHD2_KMT2A cd15590
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...
418-460 8.67e-06

PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, CXXC-type zinc finger protein 7, myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), trithorax-like protein (Htrx), or zinc finger protein HRX) is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4 methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, a Bromodomain domain, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


Pssm-ID: 277065  Cd Length: 50  Bit Score: 44.63  E-value: 8.67e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 119591922  418 FCRVC----KDGGELLCCDACPSSYHLHCLNPPLPEIPNGE---WLCPRC 460
Cdd:cd15590     1 FCHVCgrqhQATKQLLECNKCRNSYHPECLGPNYPTKPTKKkrvWICTKC 50
PHD1_NSD1_2 cd15648
PHD finger 1 found in nuclear receptor-binding SET domain-containing protein NSD1 and NSD2; ...
419-461 1.02e-05

PHD finger 1 found in nuclear receptor-binding SET domain-containing protein NSD1 and NSD2; NSD1, also termed H3 Lysine-36 and H4 Lysine-20 specific histone-lysine N-methyltransferase, or androgen receptor coactivator 267 kDa protein, or androgen receptor-associated protein of 267 kDa, or H3-K36-HMTase H4-K20-HMTase, or Lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein, is a lysine methyltransferase that preferentially methylates H3 on Lysine36 (H3-K36) and H4 on Lysine20 (H4-K20), which is primarily associated with active transcription. It plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. It can alter transcription by interacting with the protein NSD1-interacting zinc finger protein 1 (NIZP1). It also mitigates caspase-1 activation by listeriolysin o (LLO) in macrophages, and requires functional LLO for the regulation of IL-1beta secretion. Moreover, NSD1 regulates RNA polymerase II (RNAP II) recruitment to bone morphogenetic protein 4 (BMP4). NSD2, also termed histone-lysine N-methyltransferase NSD2, or multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). Both NSD1 and NSD2 contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). In addition, NSD2 harbors a high mobility group (HMG) box. The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD fingers mediate chromatin interaction and recognition of histone marks. This model corresponds to the first PHD finger.


Pssm-ID: 277118  Cd Length: 43  Bit Score: 44.39  E-value: 1.02e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 119591922  419 CRVCKDGGELLCCDA-CPSSYHLHCLNppLPEIPNGEWLCPRCT 461
Cdd:cd15648     2 CQVCEKPGELLLCEGqCCGAFHLDCIG--LSEMPSGKFICDECI 43
PHD2_KMT2A_like cd15507
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
418-460 1.12e-05

PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


Pssm-ID: 276982  Cd Length: 50  Bit Score: 44.38  E-value: 1.12e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 119591922  418 FCRVCKDGGE----LLCCDACPSSYHLHCLNPPLPEIPNGE---WLCPRC 460
Cdd:cd15507     1 FCHVCGRKGQaqkqLLECEKCQRGYHVDCLGPSYPTKPTRKkktWICSKC 50
PHD3_NSD cd15566
PHD finger 3 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
345-386 1.57e-05

PHD finger 3 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the third PHD finger.


Pssm-ID: 277041  Cd Length: 48  Bit Score: 43.96  E-value: 1.57e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 119591922  345 YCEVCQQG-----GEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPH 386
Cdd:cd15566     1 TCATCEASgdgssGKLVRCIRCPRAYHAGCIPAGSKLLNKKLIICPK 47
PHD2_KMT2B cd15591
PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...
418-460 2.28e-05

PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed trithorax homolog 2 or WW domain-binding protein 7 (WBP-7), is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD), an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


Pssm-ID: 277066  Cd Length: 50  Bit Score: 43.39  E-value: 2.28e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 119591922  418 FCRVC----KDGGELLCCDACPSSYHLHCLNPPLPEIPNGE---WLCPRC 460
Cdd:cd15591     1 FCHVCgrknKESKPLLECERCRNCYHPACLGPNYPKPANRKkrpWICSAC 50
PHD_ING cd15505
PHD finger found in the inhibitor of growth (ING) protein family; The ING family includes a ...
345-387 3.21e-05

PHD finger found in the inhibitor of growth (ING) protein family; The ING family includes a group of tumor suppressors, ING1-5, which act as readers and writers of the histone epigenetic code, affecting DNA damage response, chromatin remodeling, cellular senescence, differentiation, cell cycle regulation and apoptosis. They may have a general role in mediating the cellular response to genotoxic stress through binding to and regulating the activities of histone acetyltransferase (HAT) and histone deacetylase (HDAC) chromatin remodeling complexes. All ING proteins contain an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 276980 [Multi-domain]  Cd Length: 45  Bit Score: 42.67  E-value: 3.21e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 119591922  345 YCeVCQQG--GEIILCDT--CPRA-YHLVCLDpeLEKAPEGKWSCPHC 387
Cdd:cd15505     1 YC-ICNQVsyGEMVACDNpnCPIEwFHFECVG--LTAKPKGKWYCPEC 45
PHD_ING3 cd15585
PHD finger found in inhibitor of growth protein 3 (ING3) and similar proteins; ING3, also ...
345-387 3.51e-05

PHD finger found in inhibitor of growth protein 3 (ING3) and similar proteins; ING3, also termed p47ING3, is one member of the inhibitor of growth (ING) family of type II tumor suppressors. It is ubiquitously expressed and has been implicated in transcription modulation, cell cycle control, and the induction of apoptosis. It is an important subunit of human NuA4 histone acetyltransferase complex, which regulates the acetylation of histones H2A and H4. Moreover, ING3 promotes ultraviolet (UV)-induced apoptosis through the Fas/caspase-8-dependent pathway in melanoma cells. It physically interacts with subunits of E3 ligase Skp1-Cullin-F-boxprotein complex (SCF complex) and is degraded by the SCF (F-box protein S-phase kinase-associated protein 2, Skp2)-mediated ubiquitin-proteasome system. It also acts as a suppression factor during tumorigenesis and progression of hepatocellular carcinoma (HCC). ING3 contains an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277060 [Multi-domain]  Cd Length: 45  Bit Score: 42.82  E-value: 3.51e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 119591922  345 YCeVCQQ--GGEIILCD--TCP-RAYHLVCLDpeLEKAPEGKWSCPHC 387
Cdd:cd15585     1 YC-ICNQvsYGEMVGCDndDCPiEWFHYGCVG--LTEAPKGKWYCPQC 45
PHD1_MTF2 cd15578
PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also ...
419-460 4.38e-05

PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also termed metal regulatory transcription factor 2, or metal-response element DNA-binding protein M96, or polycomb-like protein 2 (PCL2), complexes with the polycomb repressive complex-2 (PRC2) in embryonic stem cells and regulates the transcriptional networks during embryonic stem cell self-renewal and differentiation. It recruits the PRC2 complex to the inactive X chromosome and target loci in embryonic stem cells. Moreover, MTF2 is required for PRC2-mediated Hox cluster repression. It activates the Cdkn2a gene and promotes cellular senescence, thus suppressing the catalytic activity of PRC2 locally. MTF2 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. This model corresponds to the first PHD finger.


Pssm-ID: 277053  Cd Length: 53  Bit Score: 42.77  E-value: 4.38e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 119591922  419 CRVCKDG-----GELLCCDACPSSYHLHCLNPPLPEI---PNGEWLCPRC 460
Cdd:cd15578     2 CTVCQDGssespNEIVLCDKCGQGYHQLCHNPKIDSSvldPDVPWLCRQC 51
PHD3_PHF14 cd15563
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
419-460 4.81e-05

PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the third PHD finger.


Pssm-ID: 277038  Cd Length: 49  Bit Score: 42.38  E-value: 4.81e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 119591922  419 CRVCK---DGGELLCCDACPSSYHLHCLNPPLPEIPNGE---WLCPRC 460
Cdd:cd15563     2 CCVCKqtgDNSQLVRCDECKLCYHFGCLDPPLKKSPKQRgygWVCEEC 49
PHD_BRPF_JADE_like cd15492
PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; ...
418-460 8.24e-05

PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; The family includes BRPF proteins, Jade proteins, protein AF-10 and AF-17. BRPF proteins are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. Jade proteins are required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6, to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. AF-10, also termed ALL1 (acute lymphoblastic leukemia)-fused gene from chromosome 10 protein, is a transcription factor that has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is a putative transcription factor that may play a role in multiple signaling pathways. All Jade proteins, AF-10, and AF-17 contain a canonical PHD finger followed by a non-canonical ePHD finger. This model corresponds to the canonical PHD finger.


Pssm-ID: 276967 [Multi-domain]  Cd Length: 46  Bit Score: 41.84  E-value: 8.24e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 119591922  418 FCRVCKDGG-----ELLCCDACPSSYHLHCLNppLPEIPNGEWLCPRC 460
Cdd:cd15492     1 VCDVCLDGEseddnEIVFCDGCNVAVHQSCYG--IPLIPEGDWFCRKC 46
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
418-460 8.51e-05

PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, transcription initiation factor TFIID 140 kDa subunit (TAF140), or TAFII-140, is an integral component of TFIID) is a general initiation factor (GTF) that plays a key role in preinitiation complex (PIC) assembly through core promoter recognition. The interaction of H3K4me3 with TAF3 directs global TFIID recruitment to active genes, which regulates gene-selective functions of p53 in response to genotoxic stress. TAF3 is highly enriched in embryonic stem cells and is required for endoderm lineage differentiation and prevents premature specification of neuroectoderm and mesoderm. Moreover, TAF3, along with TRF3, forms a complex that is essential for myogenic differentiation. TAF3 contains a plant homeodomain (PHD) finger. This family also includes Drosophila melanogaster BIP2 (Bric-a-brac interacting protein 2) protein, which functions as an interacting partner of D. melanogaster p53 (Dmp53).


Pssm-ID: 276997 [Multi-domain]  Cd Length: 46  Bit Score: 41.50  E-value: 8.51e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 119591922  418 FCRVCK---DGGELLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRC 460
Cdd:cd15522     1 ICPICKkpdDGSPMIGCDECDDWYHWECVGITDEPPEEDDWFCPKC 46
ADDz_ATRX cd11726
ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked); ADDz_ATRX is a ...
417-438 8.51e-05

ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked); ADDz_ATRX is a PHD-like zinc finger domain of ATRX, which belongs to the SNF2 family of chromatin remodeling proteins. ATRX is a large chromatin-associated nuclear protein with two domains, ADDz_ATRX at the N-terminus, followed by a C-terminal ATPase/helicase domain. The ADDz_ATRX domain recognizes a specific methylated histone, and this interaction is required for heterochromatin localization of the ATRX protein. Missense mutations in either of the two ATRX domains lead to the X-linked alpha-thalassemia and mental retardation syndrome; however the mutations in the ADDz_ATRX domain produce a more severe disease phenotype that may also relate to disturbing unknown functions or interaction sites of this domain. The ADDz domain is also present in chromatin-associated proteins cytosine-5-methyltransferase 3 (Dnmt3); it is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger. PHD zinc finger domains have been identified in more than 40 proteins that are mainly involved in chromatin mediated transcriptional control; the classical PHD zinc finger has a C4-H-C3 motif that spans about 50-80 amino acids. In ADDz, the conserved histidine residue of the PHD finger is replaced by a cysteine, and an additional zinc finger C2-C2 like motif is located about twenty residues upstream of the C4-C-C3 motif.


Pssm-ID: 277252 [Multi-domain]  Cd Length: 102  Bit Score: 43.45  E-value: 8.51e-05
                          10        20
                  ....*....|....*....|..
gi 119591922  417 EFCRVCKDGGELLCCDACPSSY 438
Cdd:cd11726    51 EYCRWCGQGGDLICCDFCPNVF 72
PHD1_KMT2A_like cd15506
PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
419-460 8.71e-05

PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the first PHD finger.


Pssm-ID: 276981  Cd Length: 47  Bit Score: 41.58  E-value: 8.71e-05
                          10        20        30        40
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gi 119591922  419 CRVCKDGG--ELLCCDACPSSYHLHCLNP-PLPEIPNGE-WLCPRC 460
Cdd:cd15506     2 CFLCGSAGlnELLYCSVCCEPYHTFCLEEaERPLNINKDnWCCRRC 47
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
418-460 8.72e-05

PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the first PHD finger.


Pssm-ID: 276984  Cd Length: 48  Bit Score: 41.53  E-value: 8.72e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 119591922  418 FCRVCKDGGE---LLCCDACPSSYHLHCLNPPL---PEIPNGeWLCPRC 460
Cdd:cd15509     1 NCAVCDSPGDlsdLLFCTSCGQHYHGSCLDPAVrptPLVRAG-WQCPEC 48
CD2_tandem_CHD1-2_like cd18661
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and ...
590-625 1.14e-04

repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 and CHD2. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349308  Cd Length: 58  Bit Score: 41.52  E-value: 1.14e-04
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 119591922  590 EWMMIHRILNHSFDK---KGDVHYLIKWKDLPYDQCTWE 625
Cdd:cd18661     1 QYQIVERIIAHSPQKsaaSGYPDYLCKWQGLPYSECTWE 39
PHD_BRPF1 cd15676
PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar ...
419-464 1.16e-04

PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins; BRPF1, also termed peregrin or protein Br140, is a multi-domain protein that binds histones, mediates monocytic leukemic zinc-finger protein (MOZ)-dependent histone acetylation, and is required for Hox gene expression and segmental identity. It is a close partner of the MOZ histone acetyltransferase (HAT) complex and a novel Trithorax group (TrxG) member with a central role during development. BRPF1 is primarily a nuclear protein that has a broad tissue distribution and is abundant in testes and spermatogonia. It contains a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. BRPF1 may be involved in chromatin remodeling. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277146 [Multi-domain]  Cd Length: 62  Bit Score: 41.97  E-value: 1.16e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 119591922  419 CRVCKDG-----GELLCCDACPSSYHLHCLNppLPEIPNGEWLCPRCTCPP 464
Cdd:cd15676    10 CCICNDGecqnsNVILFCDMCNLAVHQECYG--VPYIPEGQWLCRRCLQSP 58
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
345-387 1.17e-04

PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, transcription initiation factor TFIID 140 kDa subunit (TAF140), or TAFII-140, is an integral component of TFIID) is a general initiation factor (GTF) that plays a key role in preinitiation complex (PIC) assembly through core promoter recognition. The interaction of H3K4me3 with TAF3 directs global TFIID recruitment to active genes, which regulates gene-selective functions of p53 in response to genotoxic stress. TAF3 is highly enriched in embryonic stem cells and is required for endoderm lineage differentiation and prevents premature specification of neuroectoderm and mesoderm. Moreover, TAF3, along with TRF3, forms a complex that is essential for myogenic differentiation. TAF3 contains a plant homeodomain (PHD) finger. This family also includes Drosophila melanogaster BIP2 (Bric-a-brac interacting protein 2) protein, which functions as an interacting partner of D. melanogaster p53 (Dmp53).


Pssm-ID: 276997 [Multi-domain]  Cd Length: 46  Bit Score: 41.12  E-value: 1.17e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 119591922  345 YCEVCQQ---GGEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 387
Cdd:cd15522     1 ICPICKKpddGSPMIGCDECDDWYHWECVGITDEPPEEDDWFCPKC 46
PHD_Int12 cd15501
PHD finger found in integrator complex subunit 12 (Int12) and similar proteins; Int12, also ...
419-460 1.30e-04

PHD finger found in integrator complex subunit 12 (Int12) and similar proteins; Int12, also termed IntS12, or PHD finger protein 22, is a component of integrator, a multi-protein mediator of small nuclear RNA processing. The integrator complex directly interacts with the C-terminal domain of RNA polymerase II (RNAPII) largest subunit and mediates the 3' end processing of small nuclear RNAs (snRNAs) U1 and U2. Different from other components of integrator, Int12 contains a PHD finger, which is not required for snRNA 3' end cleavage. Instead, Int12 harbors a small microdomain at its N-terminus which is necessary and sufficient for Int12 function; this microdomain facilitates Int12 binding to Int1 and promotes snRNA 3' end formation.


Pssm-ID: 276976  Cd Length: 52  Bit Score: 41.18  E-value: 1.30e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 119591922  419 CRVCKD-----GGELLCCDACPSSYHLHCLNPPLPEI----PNGEWLCPRC 460
Cdd:cd15501     2 CVVCKQmdvtsGNQLVECQECHNLYHQECHKPPVTDKdvndPRLVWYCSRC 52
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
1091-1146 1.30e-04

C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 42.31  E-value: 1.30e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 119591922 1091 AQQFCFLLSTRAGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQNKKVMIY 1146
Cdd:cd18785    20 ASSLEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGRGGKDEGEVIL 75
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
700-878 1.50e-04

DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 43.83  E-value: 1.50e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  700 LHPYQLEGL-NWLRFSWAQGTDTILAdeMGLGKTVqTIVFLYSLYKEGHSkgpyLVSAPLSTIIN-WEREFEMWAPDFYV 777
Cdd:cd17926     1 LRPYQEEALeAWLAHKNNRRGILVLP--TGSGKTL-TALALIAYLKELRT----LIVVPTDALLDqWKERFEDFLGDSSI 73
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119591922  778 vtytgdkesrsvirenefsfedNAIRSGKKvfrmkkEVQIKFHVLLTSYELITIDQAILGSI--EWACLVVDEAHRLknN 855
Cdd:cd17926    74 ----------------------GLIGGGKK------KDFDDANVVVATYQSLSNLAEEEKDLfdQFGLLIVDEAHHL--P 123
                         170       180
                  ....*....|....*....|...
gi 119591922  856 QSKFFRVLNSYKIDYKLLLTGTP 878
Cdd:cd17926   124 AKTFSEILKELNAKYRLGLTATP 146
CD1_tandem_CHD5-9_like cd18668
repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, ...
498-532 1.98e-04

repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD5, CHD6, CHD7, CHD8, and CHD9. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. CHD6, CHD7, and CHD8 enzymes have been demonstrated to have different substrate specificities and remodeling activities. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349315 [Multi-domain]  Cd Length: 68  Bit Score: 41.17  E-value: 1.98e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 119591922  498 PPPKPLEGIPEREFFVKWAGLSYWHCSWVKELQLE 532
Cdd:cd18668    19 EKEEGAEEIEVEEYLVKYKNFSYLHCEWKTEEELE 53
BAH_plant_2 cd04718
BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH ...
438-461 2.01e-04

BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240069  Cd Length: 148  Bit Score: 43.73  E-value: 2.01e-04
                          10        20
                  ....*....|....*....|....
gi 119591922  438 YHLHCLNPPLPEIPNGEWLCPRCT 461
Cdd:cd04718     2 FHLCCLRPPLKEVPEGDWICPFCE 25
PHD_BRPF2 cd15677
PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar ...
419-460 2.23e-04

PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar proteins; BRPF2, also termed bromodomain-containing protein 1 (BRD1), or BR140-like protein, is encoded by BRL (BR140 Like gene). It is responsible for the bulk of the acetylation of H3K14 and forms a novel monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with HBO1 and ING4. The complex is required for full transcriptional activation of the erythroid-specific regulator genes essential for terminal differentiation and survival of erythroblasts in fetal liver. BRPF2 shows widespread expression and localizes to the nucleus within spermatocytes. It contains a cysteine rich region harboring a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277147 [Multi-domain]  Cd Length: 54  Bit Score: 40.77  E-value: 2.23e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 119591922  419 CRVCKDG-----GELLCCDACPSSYHLHCLNppLPEIPNGEWLCPRC 460
Cdd:cd15677     4 CCICMDGecqnsNVILFCDMCNLAVHQECYG--VPYIPEGQWLCRHC 48
CD_CSD cd00024
CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this ...
596-625 2.29e-04

CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this group are chromodomains or chromo shadow domains; these are SH3-fold-beta-barrel domains of the chromo-like superfamily. Chromodomains lack the first strand of the SH3-fold-beta-barrel, this first strand is altered by insertion in the chromo shadow domains. The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. Chromodomain-containing proteins include: i) those having an N-terminal chromodomain followed by a related chromo shadow domain, such as Drosophila and human heterochromatin protein Su(var)205 (HP1), and mammalian modifier 1 and 2; ii) those having a single chromodomain, such as Drosophila protein Polycomb (Pc), mammalian modifier 3, human Mi-2 autoantigen, and several yeast and Caenorhabditis elegans proteins of unknown function; iii) those having paired tandem chromodomains, such as mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1; (iv) and elongation factor eEF3, a member of the ATP-binding cassette (ABC) family of proteins, that serves an essential function in the translation cycle of fungi. eEF3 is a soluble factor lacking a transmembrane domain and having two ABC domains arranged in tandem, with a unique chromodomain inserted within the ABC2 domain.


Pssm-ID: 349274 [Multi-domain]  Cd Length: 50  Bit Score: 40.54  E-value: 2.29e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 119591922  596 RILNHSFdKKGDVHYLIKWKDLPYDQCTWE 625
Cdd:cd00024     5 KILDHRV-RKGKLEYLVKWKGYPPEENTWE 33
BAH_plant_2 cd04718
BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH ...
365-390 3.00e-04

BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240069  Cd Length: 148  Bit Score: 42.96  E-value: 3.00e-04
                          10        20
                  ....*....|....*....|....*.
gi 119591922  365 YHLVCLDPELEKAPEGKWSCPHCEKE 390
Cdd:cd04718     2 FHLCCLRPPLKEVPEGDWICPFCEVE 27
PHD_ING5 cd15685
PHD finger found in inhibitor of growth protein 5 (ING5); ING5, also termed p28ING5, is one ...
345-390 4.33e-04

PHD finger found in inhibitor of growth protein 5 (ING5); ING5, also termed p28ING5, is one member of the inhibitor of growth (ING) family of type II tumor suppressors. It acts as a Tip60 cofactor that acetylates p53 at K120 and subsequently activates the expression of p53-dependent apoptotic genes in response to DNA damage. Aberrant ING5 expression may contribute to pathogenesis, growth, and invasion of gastric carcinomas and colorectal cancer. ING5 can physically interact with p300 and p53 in vivo, and its overexpression induces apoptosis in colorectal cancer cells. It also associates with cyclin A1 (INCA1) and functions as a growth suppressor with suppressed expression in Acute Myeloid Leukemia (AML). Moreover, ING5 translocation from the nucleus to the cytoplasm might be a critical event for carcinogenesis and tumor progression in human head and neck squamous cell carcinoma. In addition, ING5 associates with histone acetyltransferase (HAT) complexes containing MOZ (monocytic leukemia zinc finger protein)/MORF (MOZ-related factor) and HBO1, and further directs the MOZ/MORF and HBO1 complexes to chromatin. ING5 contains an N-terminal ING histone-binding domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277155 [Multi-domain]  Cd Length: 49  Bit Score: 39.65  E-value: 4.33e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 119591922  345 YCeVCQQ--GGEIILCDT--CP-RAYHLVCLDpeLEKAPEGKWSCPHCEKE 390
Cdd:cd15685     2 YC-LCHQvsYGEMIGCDNpdCPiEWFHFACVD--LTTKPKGKWFCPRCTQE 49
PHD_ING3 cd15585
PHD finger found in inhibitor of growth protein 3 (ING3) and similar proteins; ING3, also ...
426-460 5.56e-04

PHD finger found in inhibitor of growth protein 3 (ING3) and similar proteins; ING3, also termed p47ING3, is one member of the inhibitor of growth (ING) family of type II tumor suppressors. It is ubiquitously expressed and has been implicated in transcription modulation, cell cycle control, and the induction of apoptosis. It is an important subunit of human NuA4 histone acetyltransferase complex, which regulates the acetylation of histones H2A and H4. Moreover, ING3 promotes ultraviolet (UV)-induced apoptosis through the Fas/caspase-8-dependent pathway in melanoma cells. It physically interacts with subunits of E3 ligase Skp1-Cullin-F-boxprotein complex (SCF complex) and is degraded by the SCF (F-box protein S-phase kinase-associated protein 2, Skp2)-mediated ubiquitin-proteasome system. It also acts as a suppression factor during tumorigenesis and progression of hepatocellular carcinoma (HCC). ING3 contains an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277060 [Multi-domain]  Cd Length: 45  Bit Score: 39.36  E-value: 5.56e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 119591922  426 GELLCCD--ACPSS-YHLHCLNppLPEIPNGEWLCPRC 460
Cdd:cd15585    10 GEMVGCDndDCPIEwFHYGCVG--LTEAPKGKWYCPQC 45
PHD_BRPF3 cd15678
PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and similar ...
418-466 6.66e-04

PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and similar proteins; BRPF3 is a homolog of BRPF1 and BRPF2. It is a scaffold protein that forms a novel monocytic leukemic zinc finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with other regulatory subunits. BRPF3 contains a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277148 [Multi-domain]  Cd Length: 55  Bit Score: 39.62  E-value: 6.66e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 119591922  418 FCRVCKD-----GGELLCCDACPSSYHLHCLNppLPEIPNGEWLCPRCTCPPLK 466
Cdd:cd15678     3 FCCVCLDdechnSNVILFCDICNLAVHQECYG--VPYIPEGQWLCRCCLQSPSR 54
PHD_ING4_5 cd15586
PHD finger found in inhibitor of growth protein 4 (ING4) and 5 (ING5); ING4, also termed ...
345-387 9.23e-04

PHD finger found in inhibitor of growth protein 4 (ING4) and 5 (ING5); ING4, also termed p29ING4, and ING5, also termed p28ING5, belong to the inhibitor of growth (ING) family of type II tumor suppressors. ING4 acts as an E3 ubiquitin ligase to induce ubiquitination of the p65 subunit of NF-kappaB and inhibit the transactivation of NF-kappaB target genes. It also induces apoptosis through a p53 dependent pathway, including increasing p53 acetylation, inhibiting Mdm2-mediated degradation of p53 and enhancing the expression of p53 responsive genes both at the transcriptional and post-translational levels. Moreover, ING4 can inhibit the translation of proto-oncogene MYC by interacting with AUF1. It also regulates other transcription factors, such as hypoxia-inducible factor (HIF). ING5 is a Tip60 cofactor that acetylates p53 at K120 and subsequently activates the expression of p53-dependent apoptotic genes in response to DNA damage. Aberrant ING5 expression may contribute to pathogenesis, growth, and invasion of gastric carcinomas and colorectal cancer. ING5 can physically interact with p300 and p53 in vivo, and its overexpression induces apoptosis in colorectal cancer cells. It also associates with cyclin A1 (INCA1) and functions as a growth suppressor with suppressed expression in Acute Myeloid Leukemia (AML). Moreover, ING5 translocation from the nucleus to the cytoplasm might be a critical event for carcinogenesis and tumor progression in human head and neck squamous cell carcinoma. Both ING4 and ING5 contain an N-terminal ING histone-binding domain and a C-terminal plant homeodomain (PHD) finger. They associate with histone acetyltransferase (HAT) complexes containing MOZ (monocytic leukemia zinc finger protein)/MORF (MOZ-related factor) and HBO1, and further direct the MOZ/MORF and HBO1 complexes to chromatin.


Pssm-ID: 277061 [Multi-domain]  Cd Length: 45  Bit Score: 38.71  E-value: 9.23e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 119591922  345 YCeVCQQ--GGEIILCDT--CP-RAYHLVCLDpeLEKAPEGKWSCPHC 387
Cdd:cd15586     1 YC-LCHQvsYGEMIGCDNpdCPiEWFHFACVG--LTTKPKGKWFCPRC 45
PHD_BRPF2 cd15677
PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar ...
349-387 9.66e-04

PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar proteins; BRPF2, also termed bromodomain-containing protein 1 (BRD1), or BR140-like protein, is encoded by BRL (BR140 Like gene). It is responsible for the bulk of the acetylation of H3K14 and forms a novel monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with HBO1 and ING4. The complex is required for full transcriptional activation of the erythroid-specific regulator genes essential for terminal differentiation and survival of erythroblasts in fetal liver. BRPF2 shows widespread expression and localizes to the nucleus within spermatocytes. It contains a cysteine rich region harboring a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277147 [Multi-domain]  Cd Length: 54  Bit Score: 38.84  E-value: 9.66e-04
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 119591922  349 CQQGGEIILCDTCPRAYHLVCLDpeLEKAPEGKWSCPHC 387
Cdd:cd15677    12 CQNSNVILFCDMCNLAVHQECYG--VPYIPEGQWLCRHC 48
ADDz cd11672
ATRX, Dnmt3 and Dnmt3l PHD-like zinc finger domain (ADDz); The ADDz zinc finger domain is ...
334-387 1.03e-03

ATRX, Dnmt3 and Dnmt3l PHD-like zinc finger domain (ADDz); The ADDz zinc finger domain is present in the chromatin-associated proteins cytosine-5-methyltransferase 3 (Dnmt3) and ATRX, a SNF2 type transcription factor protein. The Dnmt3 family includes two active DNA methyltransferases, Dnmt3a and -3b, and one regulatory factor Dnmt3l. DNA methylation is an important epigenetic mechanism involved in diverse biological processes such as embryonic development, gene expression, and genomic imprinting. The ADDz domain is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger. PHD zinc finger domains have been identified in more than 40 proteins that are mainly involved in chromatin mediated transcriptional control; the classical PHD zinc finger has a C4-H-C3 motif that spans about 50-80 amino acids. In ADDz, the conserved histidine residue of the PHD finger is replaced by a cysteine, and an additional zinc finger C2-C2 like motif is located about twenty residues upstream of the C4-C-C3 motif.


Pssm-ID: 277250 [Multi-domain]  Cd Length: 99  Bit Score: 40.24  E-value: 1.03e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 119591922  334 DGDGYetdhQDYCEVCQQGGEIILCDT--CPRAYHLVCLDP-----ELEKA-PEGKWSCPHC 387
Cdd:cd11672    40 DDDGY----QSYCRICCEGGNLLCCGNnfCHRCFCKECVDRlvgpgELSTMdENNQWYCYIC 97
PHD_ING1_2 cd15584
PHD finger found in inhibitor of growth protein 1 (ING1) and 2 (ING2); ING1 is an epigenetic ...
345-387 1.11e-03

PHD finger found in inhibitor of growth protein 1 (ING1) and 2 (ING2); ING1 is an epigenetic regulator and a type II tumor suppressor that impacts cell growth, aging, apoptosis, and DNA repair, by affecting chromatin conformation and gene expression. It acts as a reader of the active chromatin mark, the trimethylation of histone H3 lysine 4 (H3K4me3). It binds and directs Growth arrest and DNA damage inducible protein 45 a (Gadd45a) to target sites, thus linking the histone code with DNA demethylation. It interacts with the proliferating cell nuclear antigen (PCNA) via the PCNA-interacting protein (PIP) domain in a UV-inducible manner. It also interacts with a PCNA-interacting protein, p15 (PAF). Moreover, ING1 associates with members of the 14-3-3 family, which is necessary for cytoplasmic relocalization. Endogenous ING1 protein specifically interacts with the pro-apoptotic BCL2 family member BAX and colocalizes with BAX in a UV-inducible manner. It stabilizes the p53 tumor suppressor by inhibiting polyubiquitination of multi-monoubiquitinated forms via interaction with and colocalization of the herpesvirus-associated ubiquitin-specific protease (HAUSP)-deubiquitinase with p53. It is also involved in trichostatin A-induced apoptosis and caspase 3 signaling in p53-deficient glioblastoma cells. In addition, tyrosine kinase Src can bind and phosphorylate ING1 and further regulates its activity. ING2, also termed inhibitor of growth 1-like protein (ING1Lp), or p32, or p33ING2, belongs to the inhibitor of growth (ING) family of type II tumor suppressors. It is a core component of a multi-factor chromatin-modifying complex containing the transcriptional co-repressor SIN3A and histone deacetylase 1 (HDAC1). It has been implicated in the control of cell cycle, in genome stability, and in muscle differentiation. ING2 independently interacts with H3K4me3 (Histone H3 trimethylated on lysine 4) and PtdIns(5)P, and modulates crosstalk between lysine methylation and lysine acetylation on histone proteins through association with chromatin in the presence of DNA damage. It collaborates with SnoN to mediate transforming growth factor (TGF)-beta-induced Smad-dependent transcription and cellular responses. It is upregulated in colon cancer and increases invasion by enhanced MMP13 expression. It also acts as a cofactor of p300 for p53 acetylation and plays a positive regulatory role during p53-mediated replicative senescence. Both ING1 and ING2 contain an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277059 [Multi-domain]  Cd Length: 45  Bit Score: 38.58  E-value: 1.11e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 119591922  345 YCeVCQQ--GGEIILCDT--CP-RAYHLVCLDpeLEKAPEGKWSCPHC 387
Cdd:cd15584     1 YC-LCNQvsYGEMIGCDNdeCPiEWFHFSCVG--LTHKPKGKWYCPKC 45
PHD_BRPF_JADE_like cd15492
PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; ...
346-387 1.22e-03

PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; The family includes BRPF proteins, Jade proteins, protein AF-10 and AF-17. BRPF proteins are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. Jade proteins are required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6, to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. AF-10, also termed ALL1 (acute lymphoblastic leukemia)-fused gene from chromosome 10 protein, is a transcription factor that has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is a putative transcription factor that may play a role in multiple signaling pathways. All Jade proteins, AF-10, and AF-17 contain a canonical PHD finger followed by a non-canonical ePHD finger. This model corresponds to the canonical PHD finger.


Pssm-ID: 276967 [Multi-domain]  Cd Length: 46  Bit Score: 38.37  E-value: 1.22e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 119591922  346 CEVCQQGG-----EIILCDTCPRAYHLVCLDpeLEKAPEGKWSCPHC 387
Cdd:cd15492     2 CDVCLDGEseddnEIVFCDGCNVAVHQSCYG--IPLIPEGDWFCRKC 46
PHD2_KMT2A_like cd15507
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
345-387 1.32e-03

PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


Pssm-ID: 276982  Cd Length: 50  Bit Score: 38.60  E-value: 1.32e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 119591922  345 YCEVCQQGGE----IILCDTCPRAYHLVCLDPELEKAPEGK---WSCPHC 387
Cdd:cd15507     1 FCHVCGRKGQaqkqLLECEKCQRGYHVDCLGPSYPTKPTRKkktWICSKC 50
PHD_JADE cd15573
PHD finger found in proteins Jade-1, Jade-2, Jade-3, and similar proteins; This family ...
346-387 1.32e-03

PHD finger found in proteins Jade-1, Jade-2, Jade-3, and similar proteins; This family includes proteins Jade-1 (PHF17), Jade-2 (PHF15), and Jade-3 (PHF16), each of which is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. This family also contains Drosophila melanogaster PHD finger protein rhinoceros (RNO). It is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating transcription of key EGFR/Ras pathway regulators in the Drosophila eye. All Jade proteins contain a canonical Cys4HisCys3 PHD finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277048 [Multi-domain]  Cd Length: 46  Bit Score: 38.16  E-value: 1.32e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 119591922  346 CEVCQ-----QGGEIILCDTCPRAYHLVCLDpeLEKAPEGKWSCPHC 387
Cdd:cd15573     2 CDVCRspdseEGNEMVFCDKCNICVHQACYG--IQKIPEGSWLCRTC 46
PHD_JADE1 cd15679
PHD finger found in protein Jade-1 and similar proteins; Jade-1, also termed PHD finger ...
346-387 1.38e-03

PHD finger found in protein Jade-1 and similar proteins; Jade-1, also termed PHD finger protein 17 (PHF17), is a novel binding partner of von Hippel-Lindau (VHL) tumor suppressor Pvhl, a key regulator of the cellular oxygen sensing pathway. It is highly expressed in renal proximal tubules. Jade-1 functions as an essential regulator of multiple cell signaling pathways. It may be involved in the serine/threonine kinase AKT/AKT1 pathway during renal cancer pathogenesis and normally prevents renal epithelial cell proliferation and transformation. It also acts as a pro-apoptotic and growth suppressive ubiquitin ligase to inhibit canonical Wnt downstream effector beta-catenin for proteasomal degradation, and as a transcription factor associated with histone acetyltransferase activity and with increased abundance of cyclin-dependent kinase inhibitor p21. Moreover, Jade-1 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex, and plays a role in epithelial cell regeneration. It has also been identified as a novel component of the nephrocystin protein (NPHP) complex and interacts with the ciliary protein nephrocystin-4 (NPHP4). Jade-1 contains a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277149 [Multi-domain]  Cd Length: 46  Bit Score: 38.52  E-value: 1.38e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 119591922  346 CEVCQQ-----GGEIILCDTCPRAYHLVCLDpeLEKAPEGKWSCPHC 387
Cdd:cd15679     2 CDVCQSpdgedGNEMVFCDKCNICVHQACYG--ILKVPEGSWLCRTC 46
PHD_JADE2 cd15680
PHD finger found in protein Jade-2 and similar proteins; Jade-2, also termed PHD finger ...
419-460 2.32e-03

PHD finger found in protein Jade-2 and similar proteins; Jade-2, also termed PHD finger protein 15 (PHF15), is a plant homeodomain (PHD) zinc finger protein that is closely related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-2 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-2 contains a canonical Cys4HisCys3 PHD finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277150 [Multi-domain]  Cd Length: 46  Bit Score: 37.68  E-value: 2.32e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 119591922  419 CRVCK-----DGGELLCCDACPSSYHLHCLNppLPEIPNGEWLCPRC 460
Cdd:cd15680     2 CDVCRspegeDGNEMVFCDKCNVCVHQACYG--ILKVPTGSWLCRTC 46
PHD1_NSD cd15564
PHD finger 1 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
419-461 2.37e-03

PHD finger 1 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the first PHD finger.


Pssm-ID: 277039  Cd Length: 43  Bit Score: 37.70  E-value: 2.37e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 119591922  419 CRVCKDGGELLCCDA-CPSSYHLHCLNppLPEIPNGEWLCPRCT 461
Cdd:cd15564     2 CQICEKPGKLLTCEGpCCGHFHLDCLG--LSEQPDEPFKCDECT 43
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
346-387 2.92e-03

PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and KDM5B, and other similar proteins; TCF-19 was identified as a putative trans-activating factor with expression beginning at the late G1-S boundary in dividing cells. It functions as a novel islet factor necessary for proliferation and survival in the INS-1 beta cell line. It plays an important role in susceptibility to both Type 1 Diabetes Mellitus (T1DM) and Type 2 Diabetes Mellitus (T2DM); it has been suggested that it may positively impact beta cell mass under conditions of beta cell stress and increased insulin demand. KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interaction with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. This family also includes Caenorhabditis elegans Lysine-specific demethylase 7 homolog (ceKDM7A). ceKDM7A (also termed JmjC domain-containing protein 1.2, PHD finger protein 8 homolog, or PHF8 homolog) is a plant homeodomain (PHD)- and JmjC domain-containing protein that functions as a histone demethylase specific for H3K9me2 and H3K27me2. The binding of the PHD finger to H3K4me3 guides H3K9me2- and H3K27me2-specific demethylation by its catalytic JmjC domain in a trans-histone regulation mechanism. In addition, this family includes plant protein OBERON 1 and OBERON 2, Alfin1-like (AL) proteins, histone acetyltransferases (HATs) HAC, and AT-rich interactive domain-containing protein 4 (ARID4).


Pssm-ID: 276992 [Multi-domain]  Cd Length: 49  Bit Score: 37.53  E-value: 2.92e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 119591922  346 CEVCQQGGEI-----ILCDTCPRAYHLVC--LDPElEKAPEGKWSCPHC 387
Cdd:cd15517     2 CGICNLETAAvdelwVQCDGCDKWFHQFClgLSNE-RYADEDKFKCPNC 49
PHD_ING cd15505
PHD finger found in the inhibitor of growth (ING) protein family; The ING family includes a ...
426-460 2.96e-03

PHD finger found in the inhibitor of growth (ING) protein family; The ING family includes a group of tumor suppressors, ING1-5, which act as readers and writers of the histone epigenetic code, affecting DNA damage response, chromatin remodeling, cellular senescence, differentiation, cell cycle regulation and apoptosis. They may have a general role in mediating the cellular response to genotoxic stress through binding to and regulating the activities of histone acetyltransferase (HAT) and histone deacetylase (HDAC) chromatin remodeling complexes. All ING proteins contain an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 276980 [Multi-domain]  Cd Length: 45  Bit Score: 37.28  E-value: 2.96e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 119591922  426 GELLCCD--ACPSS-YHLHCLNppLPEIPNGEWLCPRC 460
Cdd:cd15505    10 GEMVACDnpNCPIEwFHFECVG--LTAKPKGKWYCPEC 45
PHD2_KMT2A cd15590
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...
345-387 2.99e-03

PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, CXXC-type zinc finger protein 7, myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), trithorax-like protein (Htrx), or zinc finger protein HRX) is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4 methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, a Bromodomain domain, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


Pssm-ID: 277065  Cd Length: 50  Bit Score: 37.31  E-value: 2.99e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 119591922  345 YCEVC----QQGGEIILCDTCPRAYHLVCLDPELEKAPEGK---WSCPHC 387
Cdd:cd15590     1 FCHVCgrqhQATKQLLECNKCRNSYHPECLGPNYPTKPTKKkrvWICTKC 50
PHD1_NSD3 cd15649
PHD finger 1 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed ...
419-460 3.99e-03

PHD finger 1 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed histone-lysine N-methyltransferase NSD3, or protein whistle, or WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, or Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1-like protein 1, or WHSC1L1), is a lysine methyltransferase encoded by gene NSD3, which is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD3 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, five plant-homeodomain (PHD) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the first PHD finger.


Pssm-ID: 277119  Cd Length: 44  Bit Score: 37.05  E-value: 3.99e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 119591922  419 CRVCKDGGELL--CCDACPSSYHLHCLNppLPEIPNGEWLCPRC 460
Cdd:cd15649     2 CQVCESFGESLvtCEGECCGLFHLECLG--LTSLPDEKFICQEC 43
PHD_JADE3 cd15681
PHD finger found in protein Jade-3 and similar proteins; Jade-3, also termed PHD finger ...
346-387 4.70e-03

PHD finger found in protein Jade-3 and similar proteins; Jade-3, also termed PHD finger protein 16 (PHF16), is a plant homeodomain (PHD) zinc finger protein that is closely related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-3 is required for ING4 and ING5 to associate with histone acetyl transferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-3 contains a canonical Cys4HisCys3 PHD domain followed by a non-canonical extended PHD (ePHD) domain, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277151 [Multi-domain]  Cd Length: 50  Bit Score: 36.87  E-value: 4.70e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 119591922  346 CEVC-----QQGGEIILCDTCPRAYHLVCLDpeLEKAPEGKWSCPHC 387
Cdd:cd15681     2 CDVCrspdsEEGNDMVFCDKCNICVHQACYG--ILKVPEGSWLCRTC 46
CD1_tandem_CHD1-2_like cd18666
repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and ...
603-625 6.03e-03

repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 and CHD2. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349313  Cd Length: 85  Bit Score: 37.66  E-value: 6.03e-03
                          10        20
                  ....*....|....*....|...
gi 119591922  603 DKKGDVHYLIKWKDLPYDQCTWE 625
Cdd:cd18666    42 DEETEIQYLIKWKGWSHIHNTWE 64
PHD_JADE cd15573
PHD finger found in proteins Jade-1, Jade-2, Jade-3, and similar proteins; This family ...
419-460 6.18e-03

PHD finger found in proteins Jade-1, Jade-2, Jade-3, and similar proteins; This family includes proteins Jade-1 (PHF17), Jade-2 (PHF15), and Jade-3 (PHF16), each of which is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. This family also contains Drosophila melanogaster PHD finger protein rhinoceros (RNO). It is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating transcription of key EGFR/Ras pathway regulators in the Drosophila eye. All Jade proteins contain a canonical Cys4HisCys3 PHD finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277048 [Multi-domain]  Cd Length: 46  Bit Score: 36.62  E-value: 6.18e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 119591922  419 CRVCK-----DGGELLCCDACPSSYHLHCLNppLPEIPNGEWLCPRC 460
Cdd:cd15573     2 CDVCRspdseEGNEMVFCDKCNICVHQACYG--IQKIPEGSWLCRTC 46
PHD_JADE1 cd15679
PHD finger found in protein Jade-1 and similar proteins; Jade-1, also termed PHD finger ...
419-460 6.42e-03

PHD finger found in protein Jade-1 and similar proteins; Jade-1, also termed PHD finger protein 17 (PHF17), is a novel binding partner of von Hippel-Lindau (VHL) tumor suppressor Pvhl, a key regulator of the cellular oxygen sensing pathway. It is highly expressed in renal proximal tubules. Jade-1 functions as an essential regulator of multiple cell signaling pathways. It may be involved in the serine/threonine kinase AKT/AKT1 pathway during renal cancer pathogenesis and normally prevents renal epithelial cell proliferation and transformation. It also acts as a pro-apoptotic and growth suppressive ubiquitin ligase to inhibit canonical Wnt downstream effector beta-catenin for proteasomal degradation, and as a transcription factor associated with histone acetyltransferase activity and with increased abundance of cyclin-dependent kinase inhibitor p21. Moreover, Jade-1 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex, and plays a role in epithelial cell regeneration. It has also been identified as a novel component of the nephrocystin protein (NPHP) complex and interacts with the ciliary protein nephrocystin-4 (NPHP4). Jade-1 contains a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277149 [Multi-domain]  Cd Length: 46  Bit Score: 36.59  E-value: 6.42e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 119591922  419 CRVCK-----DGGELLCCDACPSSYHLHCLNppLPEIPNGEWLCPRC 460
Cdd:cd15679     2 CDVCQspdgeDGNEMVFCDKCNICVHQACYG--ILKVPEGSWLCRTC 46
CD2_tandem_ScCHD1_like cd18664
repeat 2 of the paired tandem chromodomains of yeast chromodomain helicase DNA-binding protein ...
603-625 6.96e-03

repeat 2 of the paired tandem chromodomains of yeast chromodomain helicase DNA-binding protein 1, and similar proteins; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349311  Cd Length: 59  Bit Score: 36.87  E-value: 6.96e-03
                          10        20
                  ....*....|....*....|...
gi 119591922  603 DKKGDVHYLIKWKDLPYDQCTWE 625
Cdd:cd18664    18 DGTSQLQYLVKWRRLNYDECTWE 40
PHD_ING1 cd15682
PHD finger found in inhibitor of growth protein 1 (ING1); ING1 is an epigenetic regulator and ...
345-390 6.96e-03

PHD finger found in inhibitor of growth protein 1 (ING1); ING1 is an epigenetic regulator and a type II tumor suppressor that impacts cell growth, aging, apoptosis, and DNA repair, by affecting chromatin conformation and gene expression. It acts as a reader of the active chromatin mark, the trimethylation of histone H3 lysine 4 (H3K4me3). It binds and directs Growth arrest and DNA damage inducible protein 45 a (Gadd45a) to target sites, thus linking the histone code with DNA demethylation. It interacts with the proliferating cell nuclear antigen (PCNA) via the PCNA-interacting protein (PIP) domain in a UV-inducible manner. It also interacts with a PCNA-interacting protein, p15 (PAF). Moreover, ING1 associates with members of the 14-3-3 family, which is necessary for the cytoplasmic relocalization. Endogenous ING1 protein specifically interacts with the pro-apoptotic BCL2 family member BAX and colocalizes with BAX in a UV-inducible manner. It stabilizes the p53 tumor suppressor by inhibiting polyubiquitination of multi-monoubiquitinated forms via interaction with and colocalization of the herpesvirus-associated ubiquitin-specific protease (HAUSP)-deubiquitinase with p53. It is also involved in trichostatin A-induced apoptosis and caspase 3 signaling in p53-deficient glioblastoma cells. In addition, tyrosine kinase Src can bind phosphorylate ING1 and further regulates its activity. ING1 contains an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277152 [Multi-domain]  Cd Length: 49  Bit Score: 36.52  E-value: 6.96e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 119591922  345 YCeVCQQ--GGEIILCDT--CP-RAYHLVCLDpeLEKAPEGKWSCPHCEKE 390
Cdd:cd15682     2 YC-LCNQvsYGEMIGCDNdeCPiEWFHFSCVG--LNHKPKGKWYCPKCRGE 49
PHD2_AIRE cd15540
PHD finger 2 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
419-445 7.54e-03

PHD finger 2 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) protein, functions as a regulator of gene transcription in the thymus. It is essential for prevention of autoimmunity. AIRE plays a critical role in the induction of central tolerance. It promotes self-tolerance through tissue-specific antigen (TSA) expression. It also acts as an active regulator of chondrocyte differentiation. AIRE contains a homogeneously-staining region (HSR) or caspase-recruitment domain (CARD), a nuclear localization signal (NLS), a SAND (for Sp100, AIRE, nuclear phosphoprotein 41/75 or NucP41/75, and deformed epidermal auto regulatory factor 1 or Deaf1) domain, two plant homeodomain (PHD) fingers, and four LXXLL (where L stands for leucine) motifs. This model corresponds to the second PHD finger that may play a critical role in the activation of gene transcription.


Pssm-ID: 277015  Cd Length: 42  Bit Score: 36.03  E-value: 7.54e-03
                          10        20
                  ....*....|....*....|....*...
gi 119591922  419 CRVCKDG-GELLCCDACPSSYHLHCLNP 445
Cdd:cd15540     2 CGVCRGGrGDLLRCPQCLQAFHWHCHFP 29
PHD1_NSD cd15564
PHD finger 1 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
345-388 7.66e-03

PHD finger 1 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the first PHD finger.


Pssm-ID: 277039  Cd Length: 43  Bit Score: 36.16  E-value: 7.66e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 119591922  345 YCEVCQQGGEIILCD-TCPRAYHLVCLDPELEkaPEGKWSCPHCE 388
Cdd:cd15564     1 VCQICEKPGKLLTCEgPCCGHFHLDCLGLSEQ--PDEPFKCDECT 43
PHD_BRPF cd15572
PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF ...
349-387 8.72e-03

PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF proteins includes BRPF1, BRD1/BRPF2, and BRPF3. They are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277047 [Multi-domain]  Cd Length: 54  Bit Score: 36.44  E-value: 8.72e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 119591922  349 CQQGGEIILCDTCPRAYHLVCLDpeLEKAPEGKWSCPHC 387
Cdd:cd15572    12 CQNSNVILFCDMCNLAVHQECYG--VPYIPEGQWLCRRC 48
PHD1_KMT2B cd15589
PHD finger 1 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...
419-460 9.05e-03

PHD finger 1 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed trithorax homolog 2 or WW domain-binding protein 7 (WBP-7), is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3 lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the first PHD finger.


Pssm-ID: 277064  Cd Length: 47  Bit Score: 35.99  E-value: 9.05e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 119591922  419 CRVCKDGG--ELLCCDACPSSYHLHCLNP---PLPEiPNGEWLCPRC 460
Cdd:cd15589     2 CLLCASKGqhELLFCQVCCEPFHRFCLEEserPLPE-QEENWCCRRC 47
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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